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final_three_d_classification_classes_count:{0 TO 100}

Filter By

Current Database

  • EMDB [5767]

Current status

  • REL [5767]

Sample type

  • Complex [4905]
  • Protein [4310]
  • Ligand [2421]
  • RNA [521]
  • Virus [441]
  • Cellular component [411]
  • DNA [381]
  • Sample [64]
  • Cell [63]
  • Other [46]
  • Tissue [9]

Organism

  • Homo sapiens [1898]
  • Mus musculus [348]
  • Escherichia coli [324]
  • Synthetic construct [315]
  • Severe acute respiratory syndrome coronavirus [293]
  • Saccharomyces cerevisiae [231]
  • Escherichia coli [197]
  • Rattus norvegicus [161]
  • Oryctolagus cuniculus [141]
  • Human immunodeficiency virus 1 [106]
  • Trypanosoma brucei [91]
  • Bos taurus [90]
  • Saccharomyces cerevisiae [77]
  • Xenopus laevis [67]
  • Lama glama [61]
  • Thermus thermophilus [53]
  • Chlamydomonas reinhardtii [45]
  • Arabidopsis thaliana [38]
  • Yarrowia lipolytica [38]
  • Sus scrofa [37]
  • Escherichia coli [36]
  • Vicugna pacos [34]
  • Gallus gallus [34]
  • Mycolicibacterium smegmatis [31]
  • Enterobacteria phage t4 [30]
  • Macaca mulatta [29]
  • Euglena gracilis [28]
  • Danio rerio [25]
  • Pseudomonas phage jbd30 [24]
  • Thermococcus profundus [24]
  • Tetrahymena thermophila [24]
  • Mycobacterium tuberculosis [24]
  • Drosophila melanogaster [22]
  • Staphylococcus aureus [21]
  • Mycolicibacterium smegmatis [21]
  • Pseudomonas aeruginosa [21]
  • Porphyridium purpureum [21]
  • Ovis aries [21]
  • Geobacillus stearothermophilus [20]
  • Pseudomonas aeruginosa [20]
  • Mycobacterium tuberculosis [19]
  • Enterobacteria phage t4 [19]
  • Vibrio cholerae [19]
  • Influenza a virus [18]
  • Saccharomyces cerevisiae [18]
  • Escherichia phage ms2 [18]
  • Simian virus 40 [17]
  • Latrodectus tredecimguttatus [17]
  • Bluetongue virus [16]
  • Helicobacter pylori [16]
  • Caenorhabditis elegans [16]
  • Equus caballus [16]
  • Acetivibrio thermocellus [14]
  • Mycoplasma pneumoniae [14]
  • Dna molecule [14]
  • Severe acute respiratory syndrome coronavirus [14]
  • Salmonella enterica [14]
  • Staphylococcus phage p68 [13]
  • Spinacia oleracea [13]
  • Chikungunya virus [13]
  • Mus musculoides [13]
  • Strongylocentrotus purpuratus [13]
  • Enterovirus b [12]
  • Chaetomium thermophilum [12]
  • Aquifex aeolicus [12]
  • Enterovirus b [12]
  • Haliangium ochraceum [12]
  • Aequorea victoria [12]
  • Escherichia coli [12]
  • Chaetomium thermophilum [12]
  • Haliangium ochraceum [12]
  • Porcine circovirus 2 [12]
  • Entamoeba histolytica [11]
  • Azotobacter vinelandii [11]
  • Plasmodium falciparum [11]
  • Schizosaccharomyces pombe [11]
  • Klebsiella pneumoniae [11]
  • Xenopus borealis [11]
  • Hantaan orthohantavirus [10]
  • Nipah virus [10]
  • Vairimorpha necatrix [10]
  • Synechocystis sp. pcc 6803 [9]
  • Human immunodeficiency virus 2 [9]
  • Rhinovirus b [9]
  • Bacillus subtilis [9]
  • Clostridioides difficile [9]
  • Brevibacterium linens [9]
  • Gluconobacter japonicus [9]
  • Morbillivirus hominis [9]
  • (no species) [9]
  • Hepatitis b virus [8]
  • Escherichia phage ms2 [8]
  • Pyrococcus furiosus [8]
  • Bacillus sp. (strain ps3) [8]
  • Mesorhizobium japonicum [8]
  • Saccharolobus solfataricus [8]
  • Thermococcus kodakarensis [8]
  • Plasmodium falciparum [8]
  • Komagataella phaffii [8]
  • Amanita phalloides [8]

EM Method

  • Single-particle [5452]
  • Subtomogram averaging [315]

Resolution

  • < 2Å [53]
  • ≥ 2Å and < 3Å [1263]
  • ≥ 3Å and < 4Å [2560]
  • ≥ 4Å and < 5Å [657]
  • ≥ 5Å and < 6Å [179]
  • ≥ 6Å and < 8Å [320]
  • ≥ 8Å and < 12Å [243]
  • ≥ 12Å and < 16Å [103]
  • ≥ 16Å and < 20Å [95]
  • ≥ 20Å and < 30Å [153]
  • ≥ 30Å [133]

Model molecular weight

  • 0-50 kDa [64]
  • 50-100 kDa [180]
  • 100-250 kDa [1101]
  • 250-500 kDa [990]
  • 500-1000 kDa [623]
  • 1-2 MDa [253]
  • 2-5 MDa [269]
  • 5-10 MDa [113]
  • > 10 MDa [74]

Release Date

  • 2026 [116]
  • 2025 [1153]
  • 2024 [1030]
  • 2023 [752]
  • 2022 [699]
  • 2021 [510]
  • 2020 [508]
  • 2019 [388]
  • 2018 [240]
  • 2017 [176]
  • 2016 [141]
  • 2015 [11]
  • 2014 [9]
  • 2013 [31]
  • 2012 [1]
  • 2010 [2]

Author by name

  • Wang H [124]
  • Zhou ZH [123]
  • Fuzik T [118]
  • Plevka P [117]
  • Liu S [114]
  • Wang Y [104]
  • Xia X [104]
  • Rubinstein JL [99]
  • Zhang X [94]
  • Langousis G [90]
  • Ward AB [89]
  • Guo H [88]
  • Hill KL [88]
  • Kassem AM [88]
  • Shimogawa MM [88]
  • Wijono A [88]
  • Wohlschlegel JA [88]
  • Zhang Z [84]
  • Liu Y [80]
  • Li S [79]
  • Kato T [75]
  • Kishikawa J [75]
  • Zhang Y [73]
  • Chen M [72]
  • Chiu W [71]
  • Liu J [71]
  • Zhao Y [69]
  • Glatt S [68]
  • Sazanov LA [68]
  • Li Y [67]
  • Gati C [66]
  • Wang L [66]
  • Han GW [65]
  • Hillen HS [62]
  • Liu C [62]
  • Wang J [62]
  • Khan S [60]
  • Kishikawa JI [60]
  • Lander GC [60]
  • Acharya P [59]
  • Biela AP [58]
  • Gao Y [58]
  • Kwong PD [58]
  • Haynes BF [56]
  • Hrebik D [56]
  • Suzuki T [56]
  • Briggs JAG [55]
  • Lyumkis D [55]
  • Novacek J [54]
  • Chen S [53]
  • Edwards RJ [53]
  • Wang Q [53]
  • Chen J [52]
  • Zhang J [52]
  • Li H [51]
  • Mansouri K [51]
  • Saunders KO [51]
  • Hashiguchi T [50]
  • He Y [50]
  • Stuart DI [50]
  • Tyson AS [50]
  • Xu W [50]
  • Zhou L [50]
  • Anraku Y [49]
  • Bhabha G [49]
  • Kita S [49]
  • Maenaka K [49]
  • Potter CS [49]
  • Shi J [49]
  • Mitsuoka K [48]
  • Montefiori DC [48]
  • Carragher B [47]
  • Mascola JR [47]
  • Raunser S [47]
  • Hu Y [46]
  • Richter-dennerlein R [46]
  • Zhou T [46]
  • Chen X [44]
  • Cottrell CA [44]
  • Liu T [44]
  • Nakagawa T [44]
  • Savva CG [44]
  • Vercellino I [44]
  • Yokoyama K [44]
  • Zhang K [44]
  • Greber BJ [43]
  • Li D [43]
  • Ranjbar M [43]
  • Rawski M [43]
  • Wu M [43]
  • Aibara S [42]
  • Borgnia MJ [42]
  • Fry EE [42]
  • Janowska K [42]
  • Kuhlbrandt W [42]
  • Nakano A [42]
  • Yu Z [42]
  • Alam SM [41]
  • Lee SY [41]
  • Parks R [41]

Author by ORCID

  • Fuzik T [118]
  • Plevka P [116]
  • Zhou ZH [113]
  • Xia X [104]
  • Shimogawa MM [88]
  • Hill KL [88]
  • Langousis G [88]
  • Wang H [88]
  • Wohlschlegel JA [88]
  • Liu S [88]
  • Rubinstein JL [78]
  • Chiu W [70]
  • Guo H [64]
  • Kato T [64]
  • Hillen HS [61]
  • Kishikawa JI [60]
  • Ward AB [59]
  • Lander GC [58]
  • Hrebik D [56]
  • Kwong PD [55]
  • Sazanov LA [51]
  • Gati C [50]
  • Glatt S [49]
  • Chen M [47]
  • Edwards RJ [47]
  • Richter-dennerlein R [46]
  • Anraku Y [46]
  • Vercellino I [44]
  • Yokoyama K [44]
  • Briggs JAG [44]
  • Raunser S [42]
  • Greber BJ [42]
  • Zhou L [42]
  • Novacek J [42]
  • Biela AP [41]
  • Williamson JR [41]
  • Kita S [40]
  • Rehling P [39]
  • Finke AF [39]
  • Mansouri K [39]
  • Boshnakovska A [39]
  • Tan YZ [38]
  • Venugopal H [37]
  • Borgnia MJ [37]
  • Bhabha G [37]
  • Nakagawa T [35]
  • Bottcher B [35]
  • Li H [34]
  • Ranjbar M [34]
  • Cottrell CA [34]
  • Hu Y [34]
  • Zhang Z [34]
  • Lin TY [33]
  • Sempowski GD [33]
  • Lee SY [32]
  • Korostelev AA [32]
  • Lyumkis D [31]
  • Tilahun K [31]
  • Stokes DL [30]
  • Koziej L [30]
  • Baker D [29]
  • Maenaka K [29]
  • Oosterheert W [29]
  • Barnes CO [29]
  • Namba K [29]
  • Hurley JH [28]
  • Wang Y [28]
  • Loveland AB [28]
  • Stahlberg H [28]
  • He Y [28]
  • Gerle C [28]
  • Valentova L [28]
  • Gil-carton D [28]
  • Pfeffer S [27]
  • Xu W [27]
  • Woo CM [27]
  • Cheng Y [27]
  • Gobeil SMC [27]
  • Hauser BM [27]
  • Chung CW [27]
  • Queisser MA [27]
  • Stuart DI [27]
  • Rizvi Z [27]
  • Pantucek R [27]
  • Bai XC [27]
  • Chan KH [27]
  • Rawski M [27]
  • Benowitz AB [27]
  • Schmid MF [27]
  • Mitsuoka K [27]
  • Curnutt NM [27]
  • Tao XB [27]
  • Schneck JL [27]
  • Dippon VN [27]
  • Caradonna TM [26]
  • Grigorieff N [26]
  • Ludtke SJ [26]
  • Gatsogiannis C [26]
  • Macintyre AN [26]
  • Des Georges A [26]

Journal

  • NAT COMMUN [1078]
  • TO BE PUBLISHED [485]
  • NATURE [402]
  • BIORXIV [372]
  • PNAS [346]
  • SCIENCE [312]
  • ELIFE [309]
  • NAT STRUCT MOL BIOL [300]
  • CELL [265]
  • SCI ADV [237]
  • STRUCTURE [165]
  • MOL CELL [160]
  • NUCLEIC ACIDS RES [139]
  • COMMUN BIOL [124]
  • EMBO J [105]
  • CELL REP [104]
  • ACTA CRYSTALLOGR D STRUCT BIOL [92]
  • J BIOL CHEM [78]
  • J VIROL [62]
  • NAT CHEM BIOL [62]
  • J MOL BIOL [55]
  • PLOS PATHOG [55]
  • IUCRJ [39]
  • SCI REP [38]
  • NAT MICROBIOL [29]
  • PROTEIN SCI [28]
  • IMMUNITY [26]
  • CELL HOST MICROBE [23]
  • CELL RES [23]
  • NAT METHODS [22]
  • J.MOL.CELL.CARDIOL. [21]
  • PLOS BIOL [21]
  • INT J MOL SCI [20]
  • EMBO REP [19]
  • J STRUCT BIOL [19]
  • NAT PLANTS [19]
  • NPJ VACCINES [18]
  • FEBS J [17]
  • ACS NANO [16]
  • BIOCHEMISTRY [16]
  • COMMUN MATER [16]
  • SCI TRANSL MED [16]
  • J GEN VIROL [15]
  • ADV SCI [14]
  • GENES DEV [13]
  • J AM CHEM SOC [13]
  • CELL DISCOV [12]
  • J MED CHEM [12]
  • PNAS NEXUS [12]
  • VIRUSES [12]
  • J CELL BIOL [10]
  • LIFE SCI ALLIANCE [10]
  • MBIO [10]
  • NAT NANOTECHNOL [10]
  • NAT CATAL [9]
  • PLOS ONE [9]
  • INT J BIOL MACROMOL [8]
  • J BACTERIOL [8]
  • RES SQ [8]
  • ACS CATAL [7]
  • ANGEW CHEM INT ED ENGL [7]
  • MOL.BIOL.EVOL. [7]
  • BIOCHEM BIOPHYS RES COMMUN [6]
  • BIOCHIM BIOPHYS ACTA BIOENERG [6]
  • BIOMOLECULES [6]
  • ISCIENCE [6]
  • MACROMOL RAPID COMMUN [6]
  • MICROSCOPY [6]
  • NAT BIOTECHNOL [6]
  • PLANT COMMUN. [6]
  • BIOCHEM J [5]
  • CURR BIOL [5]
  • J IMMUNOL. [5]
  • J STRUCT BIOL X [5]
  • MICROBIOL IMMUNOL [5]
  • MSPHERE [5]
  • NAT MED [5]
  • NEURON [5]
  • PLOS NEGL TROP DIS [5]
  • SCI IMMUNOL [5]
  • SMALL [5]
  • ACTA CRYSTALLOGR F STRUCT BIOL COMMUN [4]
  • ANTIMICROB.AGENTS CHEMOTHER. [4]
  • CELL CHEM BIOL [4]
  • CELL REP MED [4]
  • CURR RES STRUCT BIOL [4]
  • ELECTROCHIM ACTA [4]
  • FRONT MOL BIOSCI [4]
  • MOL PLANT [4]
  • PROG BIOPHYS MOL BIOL [4]
  • PROTEIN CELL [4]
  • ULTRAMICROSCOPY [4]
  • BIOPHYS J [3]
  • CHEM COMMUN [3]
  • DEV CELL [3]
  • ENVIRON SCI TECHNOL. [3]
  • J INFECT [3]
  • NAT CHEM [3]
  • OPEN BIOL [3]
  • PLOS GENET [3]

Software

  • RELION [3113]
  • CRYOSPARC [2816]
  • CTFFIND [585]
  • GCTF [278]
  • FREALIGN [119]
  • WARP [117]
  • CISTEM [109]
  • EMAN [53]
  • EMAN2 [53]
  • IMOD [52]
  • COOT [50]
  • DYNAMO [50]
  • UCSF CHIMERAX [34]
  • PYTOM [33]
  • XMIPP [33]
  • PHENIX [25]
  • UCSF CHIMERA [25]
  • PEET [23]
  • SPHIRE [22]
  • SPIDER [20]
  • APPION [19]
  • CTFTILT [18]
  • EMCLARITY [14]
  • CHIMERA [13]
  • IMAGIC [13]
  • IMOD, RAPTOR, PROTOMO [13]
  • CTFFIND4 [12]
  • IMOD, DYNAMO [10]
  • CTFFIND3 [8]
  • EMIRA [8]
  • FOCUS [8]
  • SCIPION [8]
  • ISOLDE [7]
  • NOVACTF [7]
  • STOPGAP [7]
  • IMOD, PRIISM/IVE [6]
  • JSPR [6]
  • MATLAB [6]
  • TOM TOOLBOX [6]
  • XMIPP, ML, TOMO [6]
  • SIMPLE [5]
  • TOM, AV3 [5]
  • TOMOCTF [5]
  • BSOFT [4]
  • FREALIX [4]
  • MPSA [4]
  • CRYOLO [3]
  • CTFFIND3, LABEL AND SPIDER [3]
  • E2CTF.PY [3]
  • EMREADY [3]
  • I3 [3]
  • IMOD, XMIPP, TOMO3D [3]
  • M [3]
  • MOTIONCORR2 [3]
  • AV3 [2]
  • CHIMERA, SEGGER [2]
  • CTFPHASEFLIP [2]
  • EM [2]
  • ETOMO, DYNAMO [2]
  • MRC, IMOD, IVE [2]
  • SAMUEL [2]
  • ACE, CTFFIND3 [1]
  • AMIRA [1]
  • CCP4 PACKAGE [1]
  • CHIMERA, VMD, MDFF [1]
  • CTFIND3 [1]
  • FREALIGNX [1]
  • IMOD, AV3, TOM, DYNAMO [1]
  • IMOD, PEET [1]
  • IMOD, SPIDER, BSOFT [1]
  • IMOD, TOMO3D, RELION [1]
  • IMOD, XMIPP, IMAGIC [1]
  • IMOD,RAPTOR,PROTOMO [1]
  • J3DR [1]
  • JALIGN [1]
  • PROTOMO [1]
  • PYSEG [1]
  • PYTO [1]
  • REFMAC [1]
  • REION [1]
  • RSREF [1]
  • SPARX [1]
  • SPRING [1]
  • SUBTOM [1]
  • TOM [1]

Microscope

  • FEI TITAN KRIOS [3398]
  • TFS KRIOS [1162]
  • FEI TALOS ARCTICA [396]
  • TFS GLACIOS [152]
  • FEI POLARA 300 [129]
  • JEOL CRYO ARM 300 [110]
  • FEI TECNAI F20 [56]
  • FEI/PHILIPS EM420 [43]
  • TFS TALOS [41]
  • FEI TITAN [38]
  • FEI TECNAI SPIRIT [37]
  • FEI TECNAI ARCTICA [34]
  • FEI TECNAI 12 [28]
  • FEI TECNAI 20 [21]
  • FEI TECNAI F30 [19]
  • JEOL 2200FS [17]
  • JEOL 3200FSC [14]
  • JEOL CRYO ARM 200 [14]
  • JEOL 2100 [11]
  • FEI/PHILIPS CM300FEG/T [9]
  • JEOL 3200FS [9]
  • JEOL 2200FSC [7]
  • TFS TALOS F200C [7]
  • FEI/PHILIPS CM200FEG [4]
  • TFS TALOS L120C [4]
  • FEI/PHILIPS CM120T [2]
  • JEOL KYOTO-3000SFF [2]
  • OTHER [2]
  • JEOL 1200EXII [1]
  • JEOL 1230 [1]
  • JEOL 2010F [1]
  • JEOL 2100F [1]
  • SHUIMU TOTEM 300S [1]

Electron Source

  • FIELD EMISSION GUN [5612]
  • LAB6 [126]
  • OTHER [22]
  • TUNGSTEN HAIRPIN [7]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [1380]
  • GATAN K3 BIOQUANTUM 6K X 4K [1362]
  • GATAN K3 6K X 4K [1216]
  • FEI FALCON III 4K X 4K [465]
  • FEI FALCON IV 4K X 4K [456]
  • FEI FALCON II 4K X 4K [189]
  • GATAN K2 QUANTUM 4K X 4K [178]
  • TFS FALCON 4I 4K X 4K [178]
  • OTHER [71]
  • GATAN ULTRASCAN 4000 4K X 4K [52]
  • GATAN K3 BIOCONTINUUM 6K X 4K [28]
  • FEI CETA 4K X 4K [25]
  • TVIPS TEMCAM-F416 4K X 4K [24]
  • DIRECT ELECTRON DE-20 5K X 3K [17]
  • FEI EAGLE 2K X 2K [17]
  • FEI EAGLE 4K X 4K [17]
  • DIRECT ELECTRON DE-10 5K X 4K [13]
  • GATAN K2 BASE 4K X 4K [12]
  • GATAN MULTISCAN [10]
  • FEI FALCON I 4K X 4K [8]
  • TVIPS TEMCAM-F216 2K X 2K [8]
  • GATAN ULTRASCAN 1000 2K X 2K [7]
  • GENERIC TVIPS 4K X 4K [5]
  • TVIPS TEMCAM-F415 4K X 4K [5]
  • GATAN K2 4K X 4K [4]
  • GATAN K2 IS 4K X 4K [4]
  • GENERIC CCD [4]
  • KODAK SO-163 FILM [4]
  • DIRECT ELECTRON APOLLO 4K X 4K [3]
  • TVIPS TEMCAM-F224 2K X 2K [3]
  • DIRECT ELECTRON DE-64 8K X 8K [2]
  • GATAN ORIUS SC200 2K X 2K [1]
  • GATAN ORIUS SC600 2.7K X 2.7K [1]
  • GENERIC GATAN 2K X 2K [1]

External links

  • UniProt [3967]
  • PDB [3676]
  • PDBe-Kb [3653]
  • AlphaFold DB [3243]
  • InterPro [3062]
  • Gene Ontology [2881]
  • Pfam [2630]
  • ChEBI [2316]
  • ChEMBL [2103]
  • DrugBank [1930]
  • Complex Portal [1151]
  • EMPIAR [651]
  • SCOP2 [100]
  • CATH [74]
Sort by: Download
Showing 1 - 10 of 5767. Page 1 of 577
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EMD-48668
Download Map
3D View
Activated Leptotrichia buccalis Lbu CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
Release date: Feb. 25, 2026
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 9mvs

Taveneau C, Chai XH, D'Silva J, Bamert RS, Hayes BK, Calvert RW, Curwen DJ, Munder F, Martin LL, Barr JJ, Grinter R, Knott GJ

To Be Published

EMD-53567
Composite map
Download Map
3D View
An auto inhibitory loop in the MiDAC histone deacetylase complex
Release date: Feb. 25, 2026
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 9r4i

Fairall L, Sirvydis K, Turnbull RE, Knottnerus SJ, Gonchar O, Muskett FW, Jukes-Jones R, van Brussel L, van de Geer E, van Gassen K, Badenhorst P, Johnson D, Terhal PA, van Hasselt PM, van Jaarsveld RH, Schwabe JW

Nat Commun (2025) 16 pp. 10472-10472 [ Pubmed: 41290615 DOI: doi:10.1038/s41467-025-65472-x ]

EMD-55036
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3D View
Human TRPM4 ion channel in MSP2N2 lipid nanodisc in a calcium-bound state
Release date: Feb. 25, 2026
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9smk

Pugh CF, Feilen LP, Zivkovic D, Praestegaard KF, Sideris C, Borthwick NJ, de Lichtenberg C, Bolla JR, Autzen AAA, Autzen HE

Nat Commun (2025) 16 pp. 11399-11399 [ Pubmed: 41372170 DOI: doi:10.1038/s41467-025-66208-7 ]

EMD-55383
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3D View
Nutrient deprived rat neuronal 110S disome
Release date: Feb. 25, 2026
Resolution: 17.5 Å
EM Method: Subtomogram averaging

Schwarz A, Schuman EM

Science (2026) [ DOI: doi:10.1126/science.adr4287 ]

EMD-55384
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3D View
1 h nitrogen carbon starved yeast-rat-hybrid hibernating disome
Release date: Feb. 25, 2026
Resolution: 15.2 Å
EM Method: Subtomogram averaging

Schwarz A, Schuman EM

Science (2026) [ DOI: doi:10.1126/science.adr4287 ]

EMD-55385
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3D View
3-4 h cold shock chicken neuronal hibernating tetrasome
Release date: Feb. 25, 2026
Resolution: 27.5 Å
EM Method: Subtomogram averaging

Schwarz A, Schuman EM

Science (2026) [ DOI: doi:10.1126/science.adr4287 ]

EMD-65918
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3D View
Structure of HCMV UL33 in complex with human Gs protein
Release date: Feb. 25, 2026
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9wey

Drzazga AK, Suzuki S, Wouters C, Faas F, Nishikawa K, Kamegawa A, Fujiyoshi Y, Rosenkilde MM, Tsutsumi N

Commun Biol (2026) [ Pubmed: 41680497 DOI: doi:10.1038/s42003-026-09660-5 ]

EMD-70232
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3D View
CryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex
Release date: Feb. 25, 2026
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9o8p

Richman DE, Wendorff TJ, Rashid F, Beck C, Yan Q, Johnson HR, Eckerty RA, Fogg JM, Baker ML, Zechiedrich L, Berger JM

To Be Published

EMD-70239
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3D View
CryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex in partially unfolded transducer state
Release date: Feb. 25, 2026
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9o8z

Richman DE, Wendorff TJ, Rashid F, Beck C, Yan Q, Johnson HR, Eckerty RA, Fogg JM, Baker ML, Zechiedrich L, Berger JM

To Be Published

EMD-70259
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3D View
CryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex in asymmetric state
Release date: Feb. 25, 2026
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9o9m

Richman DE, Wendorff TJ, Rashid F, Beck C, Yan Q, Johnson HR, Eckerty RA, Fogg JM, Baker ML, Zechiedrich L, Berger JM

To Be Published

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Current Database

  • EMDB [5767]

Current status

  • REL [5767]

Sample type

  • Complex [4905]
  • Protein [4310]
  • Ligand [2421]
  • RNA [521]
  • Virus [441]
  • Cellular component [411]
  • DNA [381]
  • Sample [64]
  • Cell [63]
  • Other [46]
  • Tissue [9]

Organism

  • Homo sapiens [1898]
  • Mus musculus [348]
  • Escherichia coli [324]
  • Synthetic construct [315]
  • Severe acute respiratory syndrome coronavirus [293]
  • Saccharomyces cerevisiae [231]
  • Escherichia coli [197]
  • Rattus norvegicus [161]
  • Oryctolagus cuniculus [141]
  • Human immunodeficiency virus 1 [106]
  • Trypanosoma brucei [91]
  • Bos taurus [90]
  • Saccharomyces cerevisiae [77]
  • Xenopus laevis [67]
  • Lama glama [61]
  • Thermus thermophilus [53]
  • Chlamydomonas reinhardtii [45]
  • Arabidopsis thaliana [38]
  • Yarrowia lipolytica [38]
  • Sus scrofa [37]
  • Escherichia coli [36]
  • Vicugna pacos [34]
  • Gallus gallus [34]
  • Mycolicibacterium smegmatis [31]
  • Enterobacteria phage t4 [30]
  • Macaca mulatta [29]
  • Euglena gracilis [28]
  • Danio rerio [25]
  • Pseudomonas phage jbd30 [24]
  • Thermococcus profundus [24]
  • Tetrahymena thermophila [24]
  • Mycobacterium tuberculosis [24]
  • Drosophila melanogaster [22]
  • Staphylococcus aureus [21]
  • Mycolicibacterium smegmatis [21]
  • Pseudomonas aeruginosa [21]
  • Porphyridium purpureum [21]
  • Ovis aries [21]
  • Geobacillus stearothermophilus [20]
  • Pseudomonas aeruginosa [20]
  • Mycobacterium tuberculosis [19]
  • Enterobacteria phage t4 [19]
  • Vibrio cholerae [19]
  • Influenza a virus [18]
  • Saccharomyces cerevisiae [18]
  • Escherichia phage ms2 [18]
  • Simian virus 40 [17]
  • Latrodectus tredecimguttatus [17]
  • Bluetongue virus [16]
  • Helicobacter pylori [16]
  • Caenorhabditis elegans [16]
  • Equus caballus [16]
  • Acetivibrio thermocellus [14]
  • Mycoplasma pneumoniae [14]
  • Dna molecule [14]
  • Severe acute respiratory syndrome coronavirus [14]
  • Salmonella enterica [14]
  • Staphylococcus phage p68 [13]
  • Spinacia oleracea [13]
  • Chikungunya virus [13]
  • Mus musculoides [13]
  • Strongylocentrotus purpuratus [13]
  • Enterovirus b [12]
  • Chaetomium thermophilum [12]
  • Aquifex aeolicus [12]
  • Enterovirus b [12]
  • Haliangium ochraceum [12]
  • Aequorea victoria [12]
  • Escherichia coli [12]
  • Chaetomium thermophilum [12]
  • Haliangium ochraceum [12]
  • Porcine circovirus 2 [12]
  • Entamoeba histolytica [11]
  • Azotobacter vinelandii [11]
  • Plasmodium falciparum [11]
  • Schizosaccharomyces pombe [11]
  • Klebsiella pneumoniae [11]
  • Xenopus borealis [11]
  • Hantaan orthohantavirus [10]
  • Nipah virus [10]
  • Vairimorpha necatrix [10]
  • Synechocystis sp. pcc 6803 [9]
  • Human immunodeficiency virus 2 [9]
  • Rhinovirus b [9]
  • Bacillus subtilis [9]
  • Clostridioides difficile [9]
  • Brevibacterium linens [9]
  • Gluconobacter japonicus [9]
  • Morbillivirus hominis [9]
  • (no species) [9]
  • Hepatitis b virus [8]
  • Escherichia phage ms2 [8]
  • Pyrococcus furiosus [8]
  • Bacillus sp. (strain ps3) [8]
  • Mesorhizobium japonicum [8]
  • Saccharolobus solfataricus [8]
  • Thermococcus kodakarensis [8]
  • Plasmodium falciparum [8]
  • Komagataella phaffii [8]
  • Amanita phalloides [8]

EM Method

  • Single-particle [5452]
  • Subtomogram averaging [315]

Resolution

  • < 2Å [53]
  • ≥ 2Å and < 3Å [1263]
  • ≥ 3Å and < 4Å [2560]
  • ≥ 4Å and < 5Å [657]
  • ≥ 5Å and < 6Å [179]
  • ≥ 6Å and < 8Å [320]
  • ≥ 8Å and < 12Å [243]
  • ≥ 12Å and < 16Å [103]
  • ≥ 16Å and < 20Å [95]
  • ≥ 20Å and < 30Å [153]
  • ≥ 30Å [133]

Model molecular weight

  • 0-50 kDa [64]
  • 50-100 kDa [180]
  • 100-250 kDa [1101]
  • 250-500 kDa [990]
  • 500-1000 kDa [623]
  • 1-2 MDa [253]
  • 2-5 MDa [269]
  • 5-10 MDa [113]
  • > 10 MDa [74]

Release Date

  • 2026 [116]
  • 2025 [1153]
  • 2024 [1030]
  • 2023 [752]
  • 2022 [699]
  • 2021 [510]
  • 2020 [508]
  • 2019 [388]
  • 2018 [240]
  • 2017 [176]
  • 2016 [141]
  • 2015 [11]
  • 2014 [9]
  • 2013 [31]
  • 2012 [1]
  • 2010 [2]

Author by name

  • Wang H [124]
  • Zhou ZH [123]
  • Fuzik T [118]
  • Plevka P [117]
  • Liu S [114]
  • Wang Y [104]
  • Xia X [104]
  • Rubinstein JL [99]
  • Zhang X [94]
  • Langousis G [90]
  • Ward AB [89]
  • Guo H [88]
  • Hill KL [88]
  • Kassem AM [88]
  • Shimogawa MM [88]
  • Wijono A [88]
  • Wohlschlegel JA [88]
  • Zhang Z [84]
  • Liu Y [80]
  • Li S [79]
  • Kato T [75]
  • Kishikawa J [75]
  • Zhang Y [73]
  • Chen M [72]
  • Chiu W [71]
  • Liu J [71]
  • Zhao Y [69]
  • Glatt S [68]
  • Sazanov LA [68]
  • Li Y [67]
  • Gati C [66]
  • Wang L [66]
  • Han GW [65]
  • Hillen HS [62]
  • Liu C [62]
  • Wang J [62]
  • Khan S [60]
  • Kishikawa JI [60]
  • Lander GC [60]
  • Acharya P [59]
  • Biela AP [58]
  • Gao Y [58]
  • Kwong PD [58]
  • Haynes BF [56]
  • Hrebik D [56]
  • Suzuki T [56]
  • Briggs JAG [55]
  • Lyumkis D [55]
  • Novacek J [54]
  • Chen S [53]
  • Edwards RJ [53]
  • Wang Q [53]
  • Chen J [52]
  • Zhang J [52]
  • Li H [51]
  • Mansouri K [51]
  • Saunders KO [51]
  • Hashiguchi T [50]
  • He Y [50]
  • Stuart DI [50]
  • Tyson AS [50]
  • Xu W [50]
  • Zhou L [50]
  • Anraku Y [49]
  • Bhabha G [49]
  • Kita S [49]
  • Maenaka K [49]
  • Potter CS [49]
  • Shi J [49]
  • Mitsuoka K [48]
  • Montefiori DC [48]
  • Carragher B [47]
  • Mascola JR [47]
  • Raunser S [47]
  • Hu Y [46]
  • Richter-dennerlein R [46]
  • Zhou T [46]
  • Chen X [44]
  • Cottrell CA [44]
  • Liu T [44]
  • Nakagawa T [44]
  • Savva CG [44]
  • Vercellino I [44]
  • Yokoyama K [44]
  • Zhang K [44]
  • Greber BJ [43]
  • Li D [43]
  • Ranjbar M [43]
  • Rawski M [43]
  • Wu M [43]
  • Aibara S [42]
  • Borgnia MJ [42]
  • Fry EE [42]
  • Janowska K [42]
  • Kuhlbrandt W [42]
  • Nakano A [42]
  • Yu Z [42]
  • Alam SM [41]
  • Lee SY [41]
  • Parks R [41]

Author by ORCID

  • Fuzik T [118]
  • Plevka P [116]
  • Zhou ZH [113]
  • Xia X [104]
  • Shimogawa MM [88]
  • Hill KL [88]
  • Langousis G [88]
  • Wang H [88]
  • Wohlschlegel JA [88]
  • Liu S [88]
  • Rubinstein JL [78]
  • Chiu W [70]
  • Guo H [64]
  • Kato T [64]
  • Hillen HS [61]
  • Kishikawa JI [60]
  • Ward AB [59]
  • Lander GC [58]
  • Hrebik D [56]
  • Kwong PD [55]
  • Sazanov LA [51]
  • Gati C [50]
  • Glatt S [49]
  • Chen M [47]
  • Edwards RJ [47]
  • Richter-dennerlein R [46]
  • Anraku Y [46]
  • Vercellino I [44]
  • Yokoyama K [44]
  • Briggs JAG [44]
  • Raunser S [42]
  • Greber BJ [42]
  • Zhou L [42]
  • Novacek J [42]
  • Biela AP [41]
  • Williamson JR [41]
  • Kita S [40]
  • Rehling P [39]
  • Finke AF [39]
  • Mansouri K [39]
  • Boshnakovska A [39]
  • Tan YZ [38]
  • Venugopal H [37]
  • Borgnia MJ [37]
  • Bhabha G [37]
  • Nakagawa T [35]
  • Bottcher B [35]
  • Li H [34]
  • Ranjbar M [34]
  • Cottrell CA [34]
  • Hu Y [34]
  • Zhang Z [34]
  • Lin TY [33]
  • Sempowski GD [33]
  • Lee SY [32]
  • Korostelev AA [32]
  • Lyumkis D [31]
  • Tilahun K [31]
  • Stokes DL [30]
  • Koziej L [30]
  • Baker D [29]
  • Maenaka K [29]
  • Oosterheert W [29]
  • Barnes CO [29]
  • Namba K [29]
  • Hurley JH [28]
  • Wang Y [28]
  • Loveland AB [28]
  • Stahlberg H [28]
  • He Y [28]
  • Gerle C [28]
  • Valentova L [28]
  • Gil-carton D [28]
  • Pfeffer S [27]
  • Xu W [27]
  • Woo CM [27]
  • Cheng Y [27]
  • Gobeil SMC [27]
  • Hauser BM [27]
  • Chung CW [27]
  • Queisser MA [27]
  • Stuart DI [27]
  • Rizvi Z [27]
  • Pantucek R [27]
  • Bai XC [27]
  • Chan KH [27]
  • Rawski M [27]
  • Benowitz AB [27]
  • Schmid MF [27]
  • Mitsuoka K [27]
  • Curnutt NM [27]
  • Tao XB [27]
  • Schneck JL [27]
  • Dippon VN [27]
  • Caradonna TM [26]
  • Grigorieff N [26]
  • Ludtke SJ [26]
  • Gatsogiannis C [26]
  • Macintyre AN [26]
  • Des Georges A [26]

Journal

  • NAT COMMUN [1078]
  • TO BE PUBLISHED [485]
  • NATURE [402]
  • BIORXIV [372]
  • PNAS [346]
  • SCIENCE [312]
  • ELIFE [309]
  • NAT STRUCT MOL BIOL [300]
  • CELL [265]
  • SCI ADV [237]
  • STRUCTURE [165]
  • MOL CELL [160]
  • NUCLEIC ACIDS RES [139]
  • COMMUN BIOL [124]
  • EMBO J [105]
  • CELL REP [104]
  • ACTA CRYSTALLOGR D STRUCT BIOL [92]
  • J BIOL CHEM [78]
  • J VIROL [62]
  • NAT CHEM BIOL [62]
  • J MOL BIOL [55]
  • PLOS PATHOG [55]
  • IUCRJ [39]
  • SCI REP [38]
  • NAT MICROBIOL [29]
  • PROTEIN SCI [28]
  • IMMUNITY [26]
  • CELL HOST MICROBE [23]
  • CELL RES [23]
  • NAT METHODS [22]
  • J.MOL.CELL.CARDIOL. [21]
  • PLOS BIOL [21]
  • INT J MOL SCI [20]
  • EMBO REP [19]
  • J STRUCT BIOL [19]
  • NAT PLANTS [19]
  • NPJ VACCINES [18]
  • FEBS J [17]
  • ACS NANO [16]
  • BIOCHEMISTRY [16]
  • COMMUN MATER [16]
  • SCI TRANSL MED [16]
  • J GEN VIROL [15]
  • ADV SCI [14]
  • GENES DEV [13]
  • J AM CHEM SOC [13]
  • CELL DISCOV [12]
  • J MED CHEM [12]
  • PNAS NEXUS [12]
  • VIRUSES [12]
  • J CELL BIOL [10]
  • LIFE SCI ALLIANCE [10]
  • MBIO [10]
  • NAT NANOTECHNOL [10]
  • NAT CATAL [9]
  • PLOS ONE [9]
  • INT J BIOL MACROMOL [8]
  • J BACTERIOL [8]
  • RES SQ [8]
  • ACS CATAL [7]
  • ANGEW CHEM INT ED ENGL [7]
  • MOL.BIOL.EVOL. [7]
  • BIOCHEM BIOPHYS RES COMMUN [6]
  • BIOCHIM BIOPHYS ACTA BIOENERG [6]
  • BIOMOLECULES [6]
  • ISCIENCE [6]
  • MACROMOL RAPID COMMUN [6]
  • MICROSCOPY [6]
  • NAT BIOTECHNOL [6]
  • PLANT COMMUN. [6]
  • BIOCHEM J [5]
  • CURR BIOL [5]
  • J IMMUNOL. [5]
  • J STRUCT BIOL X [5]
  • MICROBIOL IMMUNOL [5]
  • MSPHERE [5]
  • NAT MED [5]
  • NEURON [5]
  • PLOS NEGL TROP DIS [5]
  • SCI IMMUNOL [5]
  • SMALL [5]
  • ACTA CRYSTALLOGR F STRUCT BIOL COMMUN [4]
  • ANTIMICROB.AGENTS CHEMOTHER. [4]
  • CELL CHEM BIOL [4]
  • CELL REP MED [4]
  • CURR RES STRUCT BIOL [4]
  • ELECTROCHIM ACTA [4]
  • FRONT MOL BIOSCI [4]
  • MOL PLANT [4]
  • PROG BIOPHYS MOL BIOL [4]
  • PROTEIN CELL [4]
  • ULTRAMICROSCOPY [4]
  • BIOPHYS J [3]
  • CHEM COMMUN [3]
  • DEV CELL [3]
  • ENVIRON SCI TECHNOL. [3]
  • J INFECT [3]
  • NAT CHEM [3]
  • OPEN BIOL [3]
  • PLOS GENET [3]

Software

  • RELION [3113]
  • CRYOSPARC [2816]
  • CTFFIND [585]
  • GCTF [278]
  • FREALIGN [119]
  • WARP [117]
  • CISTEM [109]
  • EMAN [53]
  • EMAN2 [53]
  • IMOD [52]
  • COOT [50]
  • DYNAMO [50]
  • UCSF CHIMERAX [34]
  • PYTOM [33]
  • XMIPP [33]
  • PHENIX [25]
  • UCSF CHIMERA [25]
  • PEET [23]
  • SPHIRE [22]
  • SPIDER [20]
  • APPION [19]
  • CTFTILT [18]
  • EMCLARITY [14]
  • CHIMERA [13]
  • IMAGIC [13]
  • IMOD, RAPTOR, PROTOMO [13]
  • CTFFIND4 [12]
  • IMOD, DYNAMO [10]
  • CTFFIND3 [8]
  • EMIRA [8]
  • FOCUS [8]
  • SCIPION [8]
  • ISOLDE [7]
  • NOVACTF [7]
  • STOPGAP [7]
  • IMOD, PRIISM/IVE [6]
  • JSPR [6]
  • MATLAB [6]
  • TOM TOOLBOX [6]
  • XMIPP, ML, TOMO [6]
  • SIMPLE [5]
  • TOM, AV3 [5]
  • TOMOCTF [5]
  • BSOFT [4]
  • FREALIX [4]
  • MPSA [4]
  • CRYOLO [3]
  • CTFFIND3, LABEL AND SPIDER [3]
  • E2CTF.PY [3]
  • EMREADY [3]
  • I3 [3]
  • IMOD, XMIPP, TOMO3D [3]
  • M [3]
  • MOTIONCORR2 [3]
  • AV3 [2]
  • CHIMERA, SEGGER [2]
  • CTFPHASEFLIP [2]
  • EM [2]
  • ETOMO, DYNAMO [2]
  • MRC, IMOD, IVE [2]
  • SAMUEL [2]
  • ACE, CTFFIND3 [1]
  • AMIRA [1]
  • CCP4 PACKAGE [1]
  • CHIMERA, VMD, MDFF [1]
  • CTFIND3 [1]
  • FREALIGNX [1]
  • IMOD, AV3, TOM, DYNAMO [1]
  • IMOD, PEET [1]
  • IMOD, SPIDER, BSOFT [1]
  • IMOD, TOMO3D, RELION [1]
  • IMOD, XMIPP, IMAGIC [1]
  • IMOD,RAPTOR,PROTOMO [1]
  • J3DR [1]
  • JALIGN [1]
  • PROTOMO [1]
  • PYSEG [1]
  • PYTO [1]
  • REFMAC [1]
  • REION [1]
  • RSREF [1]
  • SPARX [1]
  • SPRING [1]
  • SUBTOM [1]
  • TOM [1]

Microscope

  • FEI TITAN KRIOS [3398]
  • TFS KRIOS [1162]
  • FEI TALOS ARCTICA [396]
  • TFS GLACIOS [152]
  • FEI POLARA 300 [129]
  • JEOL CRYO ARM 300 [110]
  • FEI TECNAI F20 [56]
  • FEI/PHILIPS EM420 [43]
  • TFS TALOS [41]
  • FEI TITAN [38]
  • FEI TECNAI SPIRIT [37]
  • FEI TECNAI ARCTICA [34]
  • FEI TECNAI 12 [28]
  • FEI TECNAI 20 [21]
  • FEI TECNAI F30 [19]
  • JEOL 2200FS [17]
  • JEOL 3200FSC [14]
  • JEOL CRYO ARM 200 [14]
  • JEOL 2100 [11]
  • FEI/PHILIPS CM300FEG/T [9]
  • JEOL 3200FS [9]
  • JEOL 2200FSC [7]
  • TFS TALOS F200C [7]
  • FEI/PHILIPS CM200FEG [4]
  • TFS TALOS L120C [4]
  • FEI/PHILIPS CM120T [2]
  • JEOL KYOTO-3000SFF [2]
  • OTHER [2]
  • JEOL 1200EXII [1]
  • JEOL 1230 [1]
  • JEOL 2010F [1]
  • JEOL 2100F [1]
  • SHUIMU TOTEM 300S [1]

Electron Source

  • FIELD EMISSION GUN [5612]
  • LAB6 [126]
  • OTHER [22]
  • TUNGSTEN HAIRPIN [7]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [1380]
  • GATAN K3 BIOQUANTUM 6K X 4K [1362]
  • GATAN K3 6K X 4K [1216]
  • FEI FALCON III 4K X 4K [465]
  • FEI FALCON IV 4K X 4K [456]
  • FEI FALCON II 4K X 4K [189]
  • GATAN K2 QUANTUM 4K X 4K [178]
  • TFS FALCON 4I 4K X 4K [178]
  • OTHER [71]
  • GATAN ULTRASCAN 4000 4K X 4K [52]
  • GATAN K3 BIOCONTINUUM 6K X 4K [28]
  • FEI CETA 4K X 4K [25]
  • TVIPS TEMCAM-F416 4K X 4K [24]
  • DIRECT ELECTRON DE-20 5K X 3K [17]
  • FEI EAGLE 2K X 2K [17]
  • FEI EAGLE 4K X 4K [17]
  • DIRECT ELECTRON DE-10 5K X 4K [13]
  • GATAN K2 BASE 4K X 4K [12]
  • GATAN MULTISCAN [10]
  • FEI FALCON I 4K X 4K [8]
  • TVIPS TEMCAM-F216 2K X 2K [8]
  • GATAN ULTRASCAN 1000 2K X 2K [7]
  • GENERIC TVIPS 4K X 4K [5]
  • TVIPS TEMCAM-F415 4K X 4K [5]
  • GATAN K2 4K X 4K [4]
  • GATAN K2 IS 4K X 4K [4]
  • GENERIC CCD [4]
  • KODAK SO-163 FILM [4]
  • DIRECT ELECTRON APOLLO 4K X 4K [3]
  • TVIPS TEMCAM-F224 2K X 2K [3]
  • DIRECT ELECTRON DE-64 8K X 8K [2]
  • GATAN ORIUS SC200 2K X 2K [1]
  • GATAN ORIUS SC600 2.7K X 2.7K [1]
  • GENERIC GATAN 2K X 2K [1]

External links

  • UniProt [3967]
  • PDB [3676]
  • PDBe-Kb [3653]
  • AlphaFold DB [3243]
  • InterPro [3062]
  • Gene Ontology [2881]
  • Pfam [2630]
  • ChEBI [2316]
  • ChEMBL [2103]
  • DrugBank [1930]
  • Complex Portal [1151]
  • EMPIAR [651]
  • SCOP2 [100]
  • CATH [74]