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Current Database

  • EMDB [725]

Current status

  • REL [725]

Sample type

  • Complex [442]
  • Protein [314]
  • Ligand [186]
  • Cell [101]
  • Sample [83]
  • Virus [74]
  • Cellular component [73]
  • RNA [43]
  • DNA [41]
  • Tissue [8]
  • Other [4]

Organism

  • Homo sapiens [181]
  • Mus musculus [47]
  • Escherichia coli [35]
  • Rattus norvegicus [31]
  • Bos taurus [31]
  • Synthetic construct [19]
  • Saccharomyces cerevisiae [16]
  • Cricetus cricetus [13]
  • Chlamydomonas reinhardtii [13]
  • Streptococcus pyogenes [12]
  • Acinetobacter baumannii [10]
  • Nostoc sp. (strain pcc 7120 / sag 25.82 / utex 2576) [9]
  • Fusarium vanettenii [8]
  • Sus scrofa [8]
  • (no species) [7]
  • Severe acute respiratory syndrome coronavirus [7]
  • Schizosaccharomyces pombe [7]
  • Sus scrofa [7]
  • Staphylococcus aureus [6]
  • Chrysotila carterae [6]
  • Enterovirus d [6]
  • Escherichia coli [6]
  • Trypanosoma brucei [6]
  • Tetrahymena thermophila [6]
  • Drosophila melanogaster [6]
  • Oenococcus oeni [5]
  • Bacillus subtilis [5]
  • Oenococcus phage phioe33pa [5]
  • Streptococcus pyogenes [5]
  • Synechococcus virus syn5 [5]
  • Legionella pneumophila [5]
  • Caulobacter vibrioides [5]
  • Escherichia coli [5]
  • Oryctolagus cuniculus [5]
  • Human mastadenovirus b [4]
  • Murine leukemia virus [4]
  • Zaire ebolavirus [4]
  • Listeria monocytogenes [4]
  • Escherichia coli [4]
  • Mycolicibacterium smegmatis [4]
  • Enterobacteria phage t4 [4]
  • Plasmodium falciparum [4]
  • Dictyostelium discoideum [4]
  • Arabidopsis thaliana [4]
  • Algoriphagus machipongonensis [4]
  • Mycolicibacterium mucogenicum [4]
  • Tuwongella immobilis [4]
  • Lactococcus phage 1358 [4]
  • Chaetomium thermophilum [4]
  • Xenopus laevis [4]
  • Streptomyces coelicolor [3]
  • Rattus rattus [3]
  • Paramecium bursaria chlorella virus 1 [3]
  • Salmonella phage p22 [3]
  • Lachnospiraceae bacterium nd2006 [3]
  • Bacillus subtilis [3]
  • Acidibacillus sulfuroxidans [3]
  • Caulobacter vibrioides [3]
  • Deinococcus radiodurans [3]
  • Paracoccus denitrificans [3]
  • Mycobacterium phage bxb1 [3]
  • Chikungunya virus [3]
  • Rhizobium loti [3]
  • Guillardia theta [3]
  • Trypanosoma brucei [3]
  • Vibrio cholerae [3]
  • Hepatitis b virus [2]
  • Human papillomavirus [2]
  • Enterobacteria phage m13 [2]
  • (no species) [2]
  • Avian infectious bursal disease virus [2]
  • Unidentified influenza virus [2]
  • Human immunodeficiency virus 1 [2]
  • Bacillus cereus [2]
  • Bacterium [2]
  • Bacillus subtilis [2]
  • Klebsiella variicola [2]
  • Thermus thermophilus [2]
  • Lactococcus phage tuc2009 [2]
  • Bluetongue virus [2]
  • Pseudoalteromonas luteoviolacea [2]
  • Zea mays [2]
  • Halothece sp. (strain pcc 7418) [2]
  • Vibrio phage sio-2 [2]
  • Spodoptera frugiperda [2]
  • Guillardia theta [2]
  • Chlorocebus aethiops [2]
  • Equus caballus [2]
  • Camelus bactrianus [2]
  • Lama glama [2]
  • Cricetulus griseus [1]
  • Bacillus phage spp1 [1]
  • Escherichia phage phix174 [1]
  • West nile virus [1]
  • Gemmata obscuriglobus [1]
  • Murine leukemia virus [1]
  • Primate t-lymphotropic virus 1 [1]
  • Enterovirus c [1]
  • Enterovirus c [1]
  • Enterovirus c [1]

EM Method

  • Single-particle [334]
  • Tomography [273]
  • Subtomogram averaging [65]
  • Helical reconstruction [44]
  • Electron Crystallography [9]

Resolution

  • < 2Å [2]
  • ≥ 2Å and < 3Å [74]
  • ≥ 3Å and < 4Å [167]
  • ≥ 4Å and < 5Å [44]
  • ≥ 5Å and < 6Å [12]
  • ≥ 6Å and < 8Å [19]
  • ≥ 8Å and < 12Å [39]
  • ≥ 12Å and < 16Å [94]
  • ≥ 16Å and < 20Å [20]
  • ≥ 20Å and < 30Å [38]
  • ≥ 30Å [28]

Model molecular weight

  • 0-50 kDa [12]
  • 50-100 kDa [13]
  • 100-250 kDa [140]
  • 250-500 kDa [56]
  • 500-1000 kDa [22]
  • 1-2 MDa [15]
  • 2-5 MDa [7]
  • 5-10 MDa [9]
  • > 10 MDa [3]

Release Date

  • 2026 [47]
  • 2025 [39]
  • 2024 [79]
  • 2023 [57]
  • 2022 [103]
  • 2021 [87]
  • 2020 [49]
  • 2019 [129]
  • 2018 [24]
  • 2017 [20]
  • 2016 [16]
  • 2015 [15]
  • 2014 [13]
  • 2013 [19]
  • 2012 [11]
  • 2011 [3]
  • 2010 [5]
  • 2009 [2]
  • 2008 [1]
  • 2007 [4]
  • 2004 [1]
  • 2003 [1]

Author by name

  • Ren G [83]
  • Liu H [82]
  • Liu J [82]
  • Lei D [80]
  • Lei M [80]
  • Marino JP [80]
  • Nureki O [62]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Omura SN [34]
  • Hirano H [33]
  • Nakagawa R [26]
  • Moores CA [21]
  • Sano FK [21]
  • Yamashita K [20]
  • Weiss GL [19]
  • Mahamid J [18]
  • Kusakizako T [17]
  • Liu X [17]
  • Zhang F [17]
  • Shihoya W [16]
  • Shyng SL [15]
  • Sung MW [15]
  • Tanaka T [15]
  • Chiu W [14]
  • Shuto Y [14]
  • Driggers CM [13]
  • Elbaum M [13]
  • Hoki M [13]
  • Kise Y [13]
  • Mostofian B [13]
  • Patton BL [13]
  • Pigino G [13]
  • Russo JD [13]
  • Volkov VA [13]
  • Zhu S [13]
  • Zuckerman DM [13]
  • Goulet A [12]
  • Li S [12]
  • Liu Y [12]
  • Zhang X [12]
  • Beck M [11]
  • Cambillau C [11]
  • Grigorieff N [11]
  • Okamoto HH [11]
  • Rossmann MG [11]
  • Schmid MF [11]
  • Yu EW [11]
  • Ishiguro S [10]
  • Kobayashi K [10]
  • Major J [10]
  • Ohmori T [10]
  • Rosenfeld SS [10]
  • Su CC [10]
  • Yachie N [10]
  • Zhang J [10]
  • Aebi M [9]
  • Agard DA [9]
  • Akasaka H [9]
  • Alvarez Viar G [9]
  • Devuyst O [9]
  • Eras J [9]
  • Faendrich M [9]
  • Fandrich M [9]
  • Feldmueller M [9]
  • Feldmuller M [9]
  • Forchhammer K [9]
  • Gaubitz C [9]
  • Glockshuber R [9]
  • Hiramoto T [9]
  • Hoffmann PC [9]
  • Kelch BA [9]
  • Kieninger A [9]
  • Kieninger AK [9]
  • Kobayashi TA [9]
  • Lin C-W [9]
  • Lin CW [9]
  • Maldener I [9]
  • Mori H [9]
  • Nishimasu H [9]
  • Onishi K [9]
  • Pajak J [9]
  • Rubinstein JL [9]
  • Sauer MM [9]
  • Schmidt M [9]
  • Stanisich JJ [9]
  • Topf M [9]
  • Truck J [9]
  • Trueck J [9]
  • Varsano N [9]
  • Zyla DS [9]
  • Accardi A [8]
  • Alvarenga OE [8]
  • Alvarez L [8]
  • Annamalai K [8]
  • Baldus M [8]
  • Ban N [8]
  • Boehringer D [8]
  • Chlanda P [8]
  • Close W [8]

Author by ORCID

  • Nureki O [45]
  • Omura SN [19]
  • Itoh Y [17]
  • Kusakizako T [12]
  • Yu EW [11]
  • Elbaum M [11]
  • Shihoya W [11]
  • Yamashita K [10]
  • Sano FK [10]
  • Tanaka T [9]
  • Nishimasu H [8]
  • Zhang F [8]
  • Shuto Y [8]
  • Ohmori T [7]
  • Dogterom M [7]
  • Kashiwakura Y [7]
  • Mahamid J [6]
  • Tsai SQ [6]
  • Ishiguro S [6]
  • Stone NP [6]
  • Gaubitz C [6]
  • Beck M [6]
  • Hiramoto T [6]
  • Mori H [6]
  • Onishi K [6]
  • Ditommaso T [5]
  • Cambillau C [5]
  • Alfonse LE [5]
  • Murphy BJ [5]
  • Meile S [5]
  • Kirchweger P [5]
  • Burkolter M [5]
  • Yen IY [5]
  • Kilcher S [5]
  • Kelch BA [5]
  • Saibil HR [5]
  • Howell PL [5]
  • Le Marrec C [5]
  • Okamoto HH [5]
  • Goulet A [5]
  • Plitzko JM [5]
  • Loessner MJ [5]
  • Lill R [5]
  • Brun YV [5]
  • Kandiah E [5]
  • Whitfield GB [5]
  • Rubinstein JL [5]
  • Aiba S [5]
  • Burrows LL [5]
  • Xu J [5]
  • Muller CW [5]
  • Sano F [5]
  • Tomita A [5]
  • Steinhilper R [5]
  • Ptchelkine D [5]
  • Ohwada T [4]
  • Rutaganira FUN [4]
  • Khayat R [4]
  • Beton JG [4]
  • Walters KJ [4]
  • Chen L [4]
  • Lay K [4]
  • Parvate AD [4]
  • Aoki J [4]
  • Chen X [4]
  • Zhong FL [4]
  • Wu B [4]
  • Laube E [4]
  • Eisenstein F [4]
  • Kelch Phd Ba [4]
  • Gottlieb P [4]
  • Kuhlbrandt W [4]
  • Seifer S [4]
  • Pilhofer M [4]
  • Reversade B [4]
  • Lamers MH [4]
  • Monistrol J [4]
  • Galarza JM [4]
  • Langer JD [4]
  • Welsch S [4]
  • Luo J [4]
  • Kunetsky V [4]
  • Johnston EC [4]
  • Alfaro T [4]
  • Shyng SL [4]
  • Gouaux E [4]
  • Chiu W [4]
  • Dennehy JJ [4]
  • Hite RK [4]
  • Bukau B [4]
  • Meier-credo J [4]
  • Borsellini A [4]
  • Lien YW [4]
  • Okada Y [4]
  • Edel KM [4]
  • Islam ZM [4]
  • Kobayashi TA [4]
  • Van Der Oost J [3]
  • Hamdan SM [3]
  • Goldbach N [3]

Journal

  • NAT COMMUN [107]
  • SCI REP [83]
  • ELIFE [63]
  • PNAS [56]
  • SCIENCE [43]
  • BIORXIV [38]
  • NAT STRUCT MOL BIOL [38]
  • NATURE [36]
  • CELL [35]
  • TO BE PUBLISHED [35]
  • STRUCTURE [25]
  • J MOL BIOL [21]
  • COMMUN BIOL [14]
  • NAT MICROBIOL [13]
  • J VIROL [11]
  • MBIO [11]
  • MOL CELL [11]
  • SCI ADV [10]
  • EMBO J [7]
  • NAT CELL BIOL [7]
  • PLOS BIOL [6]
  • GENOME BIOL EVOL [5]
  • CELL HOST MICROBE [4]
  • FRONT AGRON [4]
  • ISCIENCE [4]
  • J CELL BIOL [4]
  • MICROSC MICROANAL [4]
  • NAT METHODS [4]
  • BIOMACROMOLECULES [3]
  • CELL REP [3]
  • EMBO REP [3]
  • J STRUCT BIOL [3]
  • MOL BIOL CELL [3]
  • PLOS GENET [3]
  • PROTEIN SCI [3]
  • DEV CELL [2]
  • EXPLORATION (BEIJING) [2]
  • FRONT MICROBIOL [2]
  • J BIOL CHEM [2]
  • J CELL SCI [2]
  • NAT CHEM BIOL [2]
  • NAT PLANTS [2]
  • NUCLEIC ACIDS RES [2]
  • PLANT PHYSIOL [2]
  • PNAS NEXUS [2]
  • ACTA CRYSTALLOGR D STRUCT BIOL [1]
  • ANTIB THER [1]
  • BIOMED PHARMACOTHER [1]
  • BIOMOLECULES [1]
  • BIOPHYS J [1]
  • BLOOD [1]
  • BMC STRUCT BIOL [1]
  • CELL RES [1]
  • FASEB J [1]
  • FEBS LETT [1]
  • IMMUNOHORIZONS [1]
  • INT J BIOL MACROMOL [1]
  • J AM CHEM SOC [1]
  • J CLIN INV [1]
  • J VIS EXP [1]
  • NANOTECHNOL RUSSIA [1]
  • NAT CHEM [1]
  • NPJ BIOFILMS MICROBIOMES [1]
  • PLOS PATHOG [1]
  • SCI SIGNAL [1]

Software

  • RELION [131]
  • IMOD [104]
  • CRYOSPARC [63]
  • CTFFIND [28]
  • CHIMERA [17]
  • GCTF [15]
  • EMAN2 [14]
  • PRIISM/IVE [13]
  • ETOMO [12]
  • PEET [12]
  • JSPR [10]
  • SPIDER, FREALIGN [9]
  • FREALIX [8]
  • PHENIX [8]
  • SPIDER [8]
  • CISTEM [7]
  • FREALIGN [7]
  • TOMO3D [7]
  • XMIPP [7]
  • DYNAMO [6]
  • EMAN2, SPIDER, XMIPP [6]
  • CTFPHASEFLIP [5]
  • UCSF CHIMERA [5]
  • WARP [5]
  • EMAN [4]
  • MATLAB [4]
  • SPIDER,FREALIGN [4]
  • EMAN2, XMIPP [3]
  • IMOD, EMAN, EMAN2, TOMOHUNTER [3]
  • REFMAC [3]
  • 2DX [2]
  • ARACHNID, RELION, SPIDER [2]
  • CHIMERA, FLEX-EM [2]
  • CHIMERA, O, COOT [2]
  • CTFFIND3, RELION, 1.2, 1.3 [2]
  • EM3DR2 [2]
  • EMAN AND FREALIGN [2]
  • EMAN2/SPARX, FREALIGN [2]
  • FREALIGN, UPPSALA_PACKAGE [2]
  • I3 [2]
  • MOLREP [2]
  • SITUS AND URO [2]
  • TOMOCTF [2]
  • AIMLESS [1]
  • CHIMERA FIT-IN-MAP [1]
  • CHIMERA, FLEXEM [1]
  • CHIMERA, NAMD [1]
  • COOT [1]
  • COOT, CHIMERA, NAMD MDFF, ROSETTA [1]
  • CTFFIND3, EMAN2, IHRSR, SPIDER, RELION [1]
  • CTFFIND3, RELION, 1.2 [1]
  • CTFFIND4 [1]
  • EMAN2 SPARX [1]
  • FREALIGN, RUBINSTEIN_2_REFINEMENT_PACKAGE, IMAGIC [1]
  • IMAGIC [1]
  • IMAGIC, FREALIGN [1]
  • IMAGIC-5, SPIDER [1]
  • INDIVIDUAL-PARTCILE, ELECTRON, TOMOGRPHY, IPET , AND, FETR [1]
  • IPET [1]
  • JSUBTOMO [1]
  • MANUAL [1]
  • MATLAB, SPIDER, EMAN [1]
  • MOTIONCORR, IMOD, TOMOCTF, PEET, BSOFT [1]
  • MRC [1]
  • PHASER [1]
  • POINTLESS [1]
  • PROTOMO [1]
  • RELION, IHRSR [1]
  • ROTAN, FREALIGN [1]
  • SITUS [1]
  • SPIDER, EMAN, IHRSR, BSOFT [1]
  • SPIDER, EMAN1, EMAN2 [1]
  • SPIDER, IMAGIC-5, CTFFIND3, RELION [1]
  • SUPRIM, PHOELIX, IHRSR, SPIDER, CTFFIND3, CUSTOM, EMGLUE.PY [1]
  • UCSF CHIMERA, FLEX-EM [1]
  • XMIPP AND EMAN [1]
  • XSCALE [1]

Microscope

  • FEI TITAN KRIOS [360]
  • TFS KRIOS [111]
  • ZEISS LIBRA120PLUS [83]
  • FEI TECNAI F20 [44]
  • FEI POLARA 300 [25]
  • FEI TECNAI 20 [15]
  • JEOL 3200FSC [14]
  • FEI TITAN [13]
  • FEI TECNAI F30 [12]
  • JEOL 2200FS [11]
  • FEI TECNAI 12 [7]
  • FEI TALOS ARCTICA [6]
  • JEOL CRYO ARM 300 [5]
  • JEOL 2100 [4]
  • JEOL 4000EX [4]
  • TFS TALOS [4]
  • FEI/PHILIPS CM200FEG [3]
  • TFS GLACIOS [3]
  • FEI TECNAI ARCTICA [2]
  • FEI/PHILIPS CM300FEG/T [1]
  • JEOL 2000EX [1]

Electron Source

  • FIELD EMISSION GUN [621]
  • LAB6 [95]
  • TUNGSTEN HAIRPIN [5]
  • OTHER [4]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [197]
  • GATAN K3 6K X 4K [122]
  • GATAN ULTRASCAN 4000 4K X 4K [111]
  • GATAN K3 BIOQUANTUM 6K X 4K [90]
  • GATAN K2 QUANTUM 4K X 4K [41]
  • KODAK SO-163 FILM [27]
  • FEI FALCON III 4K X 4K [19]
  • FEI FALCON IV 4K X 4K [18]
  • OTHER [15]
  • FEI FALCON II 4K X 4K [14]
  • GATAN K2 BASE 4K X 4K [10]
  • FEI EAGLE 4K X 4K [8]
  • TVIPS TEMCAM-F416 4K X 4K [8]
  • DIRECT ELECTRON DE-20 5K X 3K [7]
  • TFS FALCON 4I 4K X 4K [6]
  • FEI FALCON I 4K X 4K [5]
  • DECTRIS ARINA 0.2K X 0.2K [4]
  • GENERIC CCD [4]
  • DIRECT ELECTRON DE-12 4K X 3K [3]
  • GATAN K2 4K X 4K [3]
  • TVIPS TEMCAM-F224 2K X 2K [3]
  • TVIPS TEMCAM-F415 4K X 4K [3]
  • GATAN ORIUS SC200 2K X 2K [2]
  • GATAN ULTRASCAN 1000 2K X 2K [2]
  • GATAN K3 BIOCONTINUUM 6K X 4K [1]
  • GENERIC GATAN 4K X 4K [1]

External links

  • PDB [278]
  • UniProt [271]
  • AlphaFold DB [246]
  • PDBe-Kb [220]
  • InterPro [219]
  • Gene Ontology [194]
  • ChEBI [171]
  • Pfam [163]
  • DrugBank [162]
  • ChEMBL [144]
  • EMPIAR [79]
  • Complex Portal [59]
  • SCOP2 [8]
  • CATH [3]
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EMD-66336
Download Map
3D View
Subtomogram averaging of nucleosome core from reconstituted chromatin
CryoEM
Release date: Sept. 30, 2026
Resolution: 4.1 Å
EM Method: Subtomogram averaging

Zhang H, Li Y, Pan C, Zhu P

To Be Published

EMD-66337
Download Map
3D View
Subtomogram averaging of nucleosome core from SF9 cell chromatin
CryoEM
Release date: Sept. 30, 2026
Resolution: 5.0 Å
EM Method: Subtomogram averaging

Zhang H, Yan L, Pan C, Zhu P

To Be Published

EMD-67995
Download Map
3D View
Cryo-EM structure of Free fatty acid receptor 2 FFA2 -ARK1 with GLPG0974
Release date: Sept. 9, 2026
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 21ty
Q-score: 0.49
Similar entry percentile: 45%

Kojima A, Kawakami K, Kobayashi N, Kobayashi K, Matsui TE, Uemoto K, Gu Y, Narita TJ, Kugawa M, Fukuda M, Kato HE

Nat Struct Mol Biol (2026) 33 pp. 1393-1405 [ Pubmed: 42665663 DOI: doi:10.1038/s41594-026-01869-6 ]

EMD-76188
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3D View
In situ subtomogram average of the transition zone doublet microtubule in human airway cilia composite map
Composite map
CryoEM
Release date: Sept. 9, 2026
Resolution: 7.3 Å
EM Method: Subtomogram averaging
Fitted PDBs: 11yj
Q-score: 0.122
Similar entry percentile: 33%

Zhou H, Terbeck L, Berical A, Brunet M, Lange SM, Anderson JR, Olbrich H, Bracht DC, Wohlgemuth K, Rieck C, Raidt J, Klingauf J, Sutharsan S, Mussaffi H, Prais D, Dunphy V, Homma ST, Guichard P, Hamel V, Hawkins FJ, Omran H, Brown A

Science (2026) pp. eaei5957-eaei5957 [ Pubmed: 42721274 DOI: doi:10.1126/science.aei5957 ]

EMD-69297
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3D View
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the TS-cleaving state
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 23vu
Q-score: 0.623
Similar entry percentile: 91%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-69298
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3D View
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the NTS-cleaving state
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 23vv
Q-score: 0.581
Similar entry percentile: 86%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-69299
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3D View
Cryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.39 Å
EM Method: Single-particle
Fitted PDBs: 23vw
Q-score: 0.629
Similar entry percentile: 80%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-76718
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3D View
In situ cryo-EM structure of axonal F-actin from ghost neurons
CryoEM
Release date: Aug. 26, 2026
Resolution: 3.24 Å
EM Method: Helical reconstruction
Fitted PDBs: 12rv
Q-score: 0.504
Similar entry percentile: 68%

Bodakuntla S, Marelli J, Vasquez-Montes V, Biertumpfel C, Mizuno N

To Be Published

EMD-65978
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3D View
Raw data
EMPIAR-13446
Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
CryoEM
Release date: Aug. 12, 2026
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9whx
Q-score: 0.592
Similar entry percentile: 74%

Hiraizumi M, Athukoralage JS, Perry NT, Tsujimoto E, Shiojiri N, Nagahata N, Lee L, Sun G, Durrant MG, Chandrasekaran SS, Konermann S, Yamashita K, Hsu PD, Nishimasu H

Nature (2026) [ DOI: doi:10.1038/s41586-026-10903-y Pubmed: 42587149 ]

EMD-65979
Download Map
3D View
Raw data
EMPIAR-13446
Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the post-strand exchange state
CryoEM
Release date: Aug. 12, 2026
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9why
Q-score: 0.592
Similar entry percentile: 80%

Hiraizumi M, Athukoralage JS, Perry NT, Tsujimoto E, Shiojiri N, Nagahata N, Lee L, Sun G, Durrant MG, Chandrasekaran SS, Konermann S, Yamashita K, Hsu PD, Nishimasu H

Nature (2026) [ DOI: doi:10.1038/s41586-026-10903-y Pubmed: 42587149 ]

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Current Database

  • EMDB [725]

Current status

  • REL [725]

Sample type

  • Complex [442]
  • Protein [314]
  • Ligand [186]
  • Cell [101]
  • Sample [83]
  • Virus [74]
  • Cellular component [73]
  • RNA [43]
  • DNA [41]
  • Tissue [8]
  • Other [4]

Organism

  • Homo sapiens [181]
  • Mus musculus [47]
  • Escherichia coli [35]
  • Rattus norvegicus [31]
  • Bos taurus [31]
  • Synthetic construct [19]
  • Saccharomyces cerevisiae [16]
  • Cricetus cricetus [13]
  • Chlamydomonas reinhardtii [13]
  • Streptococcus pyogenes [12]
  • Acinetobacter baumannii [10]
  • Nostoc sp. (strain pcc 7120 / sag 25.82 / utex 2576) [9]
  • Fusarium vanettenii [8]
  • Sus scrofa [8]
  • (no species) [7]
  • Severe acute respiratory syndrome coronavirus [7]
  • Schizosaccharomyces pombe [7]
  • Sus scrofa [7]
  • Staphylococcus aureus [6]
  • Chrysotila carterae [6]
  • Enterovirus d [6]
  • Escherichia coli [6]
  • Trypanosoma brucei [6]
  • Tetrahymena thermophila [6]
  • Drosophila melanogaster [6]
  • Oenococcus oeni [5]
  • Bacillus subtilis [5]
  • Oenococcus phage phioe33pa [5]
  • Streptococcus pyogenes [5]
  • Synechococcus virus syn5 [5]
  • Legionella pneumophila [5]
  • Caulobacter vibrioides [5]
  • Escherichia coli [5]
  • Oryctolagus cuniculus [5]
  • Human mastadenovirus b [4]
  • Murine leukemia virus [4]
  • Zaire ebolavirus [4]
  • Listeria monocytogenes [4]
  • Escherichia coli [4]
  • Mycolicibacterium smegmatis [4]
  • Enterobacteria phage t4 [4]
  • Plasmodium falciparum [4]
  • Dictyostelium discoideum [4]
  • Arabidopsis thaliana [4]
  • Algoriphagus machipongonensis [4]
  • Mycolicibacterium mucogenicum [4]
  • Tuwongella immobilis [4]
  • Lactococcus phage 1358 [4]
  • Chaetomium thermophilum [4]
  • Xenopus laevis [4]
  • Streptomyces coelicolor [3]
  • Rattus rattus [3]
  • Paramecium bursaria chlorella virus 1 [3]
  • Salmonella phage p22 [3]
  • Lachnospiraceae bacterium nd2006 [3]
  • Bacillus subtilis [3]
  • Acidibacillus sulfuroxidans [3]
  • Caulobacter vibrioides [3]
  • Deinococcus radiodurans [3]
  • Paracoccus denitrificans [3]
  • Mycobacterium phage bxb1 [3]
  • Chikungunya virus [3]
  • Rhizobium loti [3]
  • Guillardia theta [3]
  • Trypanosoma brucei [3]
  • Vibrio cholerae [3]
  • Hepatitis b virus [2]
  • Human papillomavirus [2]
  • Enterobacteria phage m13 [2]
  • (no species) [2]
  • Avian infectious bursal disease virus [2]
  • Unidentified influenza virus [2]
  • Human immunodeficiency virus 1 [2]
  • Bacillus cereus [2]
  • Bacterium [2]
  • Bacillus subtilis [2]
  • Klebsiella variicola [2]
  • Thermus thermophilus [2]
  • Lactococcus phage tuc2009 [2]
  • Bluetongue virus [2]
  • Pseudoalteromonas luteoviolacea [2]
  • Zea mays [2]
  • Halothece sp. (strain pcc 7418) [2]
  • Vibrio phage sio-2 [2]
  • Spodoptera frugiperda [2]
  • Guillardia theta [2]
  • Chlorocebus aethiops [2]
  • Equus caballus [2]
  • Camelus bactrianus [2]
  • Lama glama [2]
  • Cricetulus griseus [1]
  • Bacillus phage spp1 [1]
  • Escherichia phage phix174 [1]
  • West nile virus [1]
  • Gemmata obscuriglobus [1]
  • Murine leukemia virus [1]
  • Primate t-lymphotropic virus 1 [1]
  • Enterovirus c [1]
  • Enterovirus c [1]
  • Enterovirus c [1]

EM Method

  • Single-particle [334]
  • Tomography [273]
  • Subtomogram averaging [65]
  • Helical reconstruction [44]
  • Electron Crystallography [9]

Resolution

  • < 2Å [2]
  • ≥ 2Å and < 3Å [74]
  • ≥ 3Å and < 4Å [167]
  • ≥ 4Å and < 5Å [44]
  • ≥ 5Å and < 6Å [12]
  • ≥ 6Å and < 8Å [19]
  • ≥ 8Å and < 12Å [39]
  • ≥ 12Å and < 16Å [94]
  • ≥ 16Å and < 20Å [20]
  • ≥ 20Å and < 30Å [38]
  • ≥ 30Å [28]

Model molecular weight

  • 0-50 kDa [12]
  • 50-100 kDa [13]
  • 100-250 kDa [140]
  • 250-500 kDa [56]
  • 500-1000 kDa [22]
  • 1-2 MDa [15]
  • 2-5 MDa [7]
  • 5-10 MDa [9]
  • > 10 MDa [3]

Release Date

  • 2026 [47]
  • 2025 [39]
  • 2024 [79]
  • 2023 [57]
  • 2022 [103]
  • 2021 [87]
  • 2020 [49]
  • 2019 [129]
  • 2018 [24]
  • 2017 [20]
  • 2016 [16]
  • 2015 [15]
  • 2014 [13]
  • 2013 [19]
  • 2012 [11]
  • 2011 [3]
  • 2010 [5]
  • 2009 [2]
  • 2008 [1]
  • 2007 [4]
  • 2004 [1]
  • 2003 [1]

Author by name

  • Ren G [83]
  • Liu H [82]
  • Liu J [82]
  • Lei D [80]
  • Lei M [80]
  • Marino JP [80]
  • Nureki O [62]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Omura SN [34]
  • Hirano H [33]
  • Nakagawa R [26]
  • Moores CA [21]
  • Sano FK [21]
  • Yamashita K [20]
  • Weiss GL [19]
  • Mahamid J [18]
  • Kusakizako T [17]
  • Liu X [17]
  • Zhang F [17]
  • Shihoya W [16]
  • Shyng SL [15]
  • Sung MW [15]
  • Tanaka T [15]
  • Chiu W [14]
  • Shuto Y [14]
  • Driggers CM [13]
  • Elbaum M [13]
  • Hoki M [13]
  • Kise Y [13]
  • Mostofian B [13]
  • Patton BL [13]
  • Pigino G [13]
  • Russo JD [13]
  • Volkov VA [13]
  • Zhu S [13]
  • Zuckerman DM [13]
  • Goulet A [12]
  • Li S [12]
  • Liu Y [12]
  • Zhang X [12]
  • Beck M [11]
  • Cambillau C [11]
  • Grigorieff N [11]
  • Okamoto HH [11]
  • Rossmann MG [11]
  • Schmid MF [11]
  • Yu EW [11]
  • Ishiguro S [10]
  • Kobayashi K [10]
  • Major J [10]
  • Ohmori T [10]
  • Rosenfeld SS [10]
  • Su CC [10]
  • Yachie N [10]
  • Zhang J [10]
  • Aebi M [9]
  • Agard DA [9]
  • Akasaka H [9]
  • Alvarez Viar G [9]
  • Devuyst O [9]
  • Eras J [9]
  • Faendrich M [9]
  • Fandrich M [9]
  • Feldmueller M [9]
  • Feldmuller M [9]
  • Forchhammer K [9]
  • Gaubitz C [9]
  • Glockshuber R [9]
  • Hiramoto T [9]
  • Hoffmann PC [9]
  • Kelch BA [9]
  • Kieninger A [9]
  • Kieninger AK [9]
  • Kobayashi TA [9]
  • Lin C-W [9]
  • Lin CW [9]
  • Maldener I [9]
  • Mori H [9]
  • Nishimasu H [9]
  • Onishi K [9]
  • Pajak J [9]
  • Rubinstein JL [9]
  • Sauer MM [9]
  • Schmidt M [9]
  • Stanisich JJ [9]
  • Topf M [9]
  • Truck J [9]
  • Trueck J [9]
  • Varsano N [9]
  • Zyla DS [9]
  • Accardi A [8]
  • Alvarenga OE [8]
  • Alvarez L [8]
  • Annamalai K [8]
  • Baldus M [8]
  • Ban N [8]
  • Boehringer D [8]
  • Chlanda P [8]
  • Close W [8]

Author by ORCID

  • Nureki O [45]
  • Omura SN [19]
  • Itoh Y [17]
  • Kusakizako T [12]
  • Yu EW [11]
  • Elbaum M [11]
  • Shihoya W [11]
  • Yamashita K [10]
  • Sano FK [10]
  • Tanaka T [9]
  • Nishimasu H [8]
  • Zhang F [8]
  • Shuto Y [8]
  • Ohmori T [7]
  • Dogterom M [7]
  • Kashiwakura Y [7]
  • Mahamid J [6]
  • Tsai SQ [6]
  • Ishiguro S [6]
  • Stone NP [6]
  • Gaubitz C [6]
  • Beck M [6]
  • Hiramoto T [6]
  • Mori H [6]
  • Onishi K [6]
  • Ditommaso T [5]
  • Cambillau C [5]
  • Alfonse LE [5]
  • Murphy BJ [5]
  • Meile S [5]
  • Kirchweger P [5]
  • Burkolter M [5]
  • Yen IY [5]
  • Kilcher S [5]
  • Kelch BA [5]
  • Saibil HR [5]
  • Howell PL [5]
  • Le Marrec C [5]
  • Okamoto HH [5]
  • Goulet A [5]
  • Plitzko JM [5]
  • Loessner MJ [5]
  • Lill R [5]
  • Brun YV [5]
  • Kandiah E [5]
  • Whitfield GB [5]
  • Rubinstein JL [5]
  • Aiba S [5]
  • Burrows LL [5]
  • Xu J [5]
  • Muller CW [5]
  • Sano F [5]
  • Tomita A [5]
  • Steinhilper R [5]
  • Ptchelkine D [5]
  • Ohwada T [4]
  • Rutaganira FUN [4]
  • Khayat R [4]
  • Beton JG [4]
  • Walters KJ [4]
  • Chen L [4]
  • Lay K [4]
  • Parvate AD [4]
  • Aoki J [4]
  • Chen X [4]
  • Zhong FL [4]
  • Wu B [4]
  • Laube E [4]
  • Eisenstein F [4]
  • Kelch Phd Ba [4]
  • Gottlieb P [4]
  • Kuhlbrandt W [4]
  • Seifer S [4]
  • Pilhofer M [4]
  • Reversade B [4]
  • Lamers MH [4]
  • Monistrol J [4]
  • Galarza JM [4]
  • Langer JD [4]
  • Welsch S [4]
  • Luo J [4]
  • Kunetsky V [4]
  • Johnston EC [4]
  • Alfaro T [4]
  • Shyng SL [4]
  • Gouaux E [4]
  • Chiu W [4]
  • Dennehy JJ [4]
  • Hite RK [4]
  • Bukau B [4]
  • Meier-credo J [4]
  • Borsellini A [4]
  • Lien YW [4]
  • Okada Y [4]
  • Edel KM [4]
  • Islam ZM [4]
  • Kobayashi TA [4]
  • Van Der Oost J [3]
  • Hamdan SM [3]
  • Goldbach N [3]

Journal

  • NAT COMMUN [107]
  • SCI REP [83]
  • ELIFE [63]
  • PNAS [56]
  • SCIENCE [43]
  • BIORXIV [38]
  • NAT STRUCT MOL BIOL [38]
  • NATURE [36]
  • CELL [35]
  • TO BE PUBLISHED [35]
  • STRUCTURE [25]
  • J MOL BIOL [21]
  • COMMUN BIOL [14]
  • NAT MICROBIOL [13]
  • J VIROL [11]
  • MBIO [11]
  • MOL CELL [11]
  • SCI ADV [10]
  • EMBO J [7]
  • NAT CELL BIOL [7]
  • PLOS BIOL [6]
  • GENOME BIOL EVOL [5]
  • CELL HOST MICROBE [4]
  • FRONT AGRON [4]
  • ISCIENCE [4]
  • J CELL BIOL [4]
  • MICROSC MICROANAL [4]
  • NAT METHODS [4]
  • BIOMACROMOLECULES [3]
  • CELL REP [3]
  • EMBO REP [3]
  • J STRUCT BIOL [3]
  • MOL BIOL CELL [3]
  • PLOS GENET [3]
  • PROTEIN SCI [3]
  • DEV CELL [2]
  • EXPLORATION (BEIJING) [2]
  • FRONT MICROBIOL [2]
  • J BIOL CHEM [2]
  • J CELL SCI [2]
  • NAT CHEM BIOL [2]
  • NAT PLANTS [2]
  • NUCLEIC ACIDS RES [2]
  • PLANT PHYSIOL [2]
  • PNAS NEXUS [2]
  • ACTA CRYSTALLOGR D STRUCT BIOL [1]
  • ANTIB THER [1]
  • BIOMED PHARMACOTHER [1]
  • BIOMOLECULES [1]
  • BIOPHYS J [1]
  • BLOOD [1]
  • BMC STRUCT BIOL [1]
  • CELL RES [1]
  • FASEB J [1]
  • FEBS LETT [1]
  • IMMUNOHORIZONS [1]
  • INT J BIOL MACROMOL [1]
  • J AM CHEM SOC [1]
  • J CLIN INV [1]
  • J VIS EXP [1]
  • NANOTECHNOL RUSSIA [1]
  • NAT CHEM [1]
  • NPJ BIOFILMS MICROBIOMES [1]
  • PLOS PATHOG [1]
  • SCI SIGNAL [1]

Software

  • RELION [131]
  • IMOD [104]
  • CRYOSPARC [63]
  • CTFFIND [28]
  • CHIMERA [17]
  • GCTF [15]
  • EMAN2 [14]
  • PRIISM/IVE [13]
  • ETOMO [12]
  • PEET [12]
  • JSPR [10]
  • SPIDER, FREALIGN [9]
  • FREALIX [8]
  • PHENIX [8]
  • SPIDER [8]
  • CISTEM [7]
  • FREALIGN [7]
  • TOMO3D [7]
  • XMIPP [7]
  • DYNAMO [6]
  • EMAN2, SPIDER, XMIPP [6]
  • CTFPHASEFLIP [5]
  • UCSF CHIMERA [5]
  • WARP [5]
  • EMAN [4]
  • MATLAB [4]
  • SPIDER,FREALIGN [4]
  • EMAN2, XMIPP [3]
  • IMOD, EMAN, EMAN2, TOMOHUNTER [3]
  • REFMAC [3]
  • 2DX [2]
  • ARACHNID, RELION, SPIDER [2]
  • CHIMERA, FLEX-EM [2]
  • CHIMERA, O, COOT [2]
  • CTFFIND3, RELION, 1.2, 1.3 [2]
  • EM3DR2 [2]
  • EMAN AND FREALIGN [2]
  • EMAN2/SPARX, FREALIGN [2]
  • FREALIGN, UPPSALA_PACKAGE [2]
  • I3 [2]
  • MOLREP [2]
  • SITUS AND URO [2]
  • TOMOCTF [2]
  • AIMLESS [1]
  • CHIMERA FIT-IN-MAP [1]
  • CHIMERA, FLEXEM [1]
  • CHIMERA, NAMD [1]
  • COOT [1]
  • COOT, CHIMERA, NAMD MDFF, ROSETTA [1]
  • CTFFIND3, EMAN2, IHRSR, SPIDER, RELION [1]
  • CTFFIND3, RELION, 1.2 [1]
  • CTFFIND4 [1]
  • EMAN2 SPARX [1]
  • FREALIGN, RUBINSTEIN_2_REFINEMENT_PACKAGE, IMAGIC [1]
  • IMAGIC [1]
  • IMAGIC, FREALIGN [1]
  • IMAGIC-5, SPIDER [1]
  • INDIVIDUAL-PARTCILE, ELECTRON, TOMOGRPHY, IPET , AND, FETR [1]
  • IPET [1]
  • JSUBTOMO [1]
  • MANUAL [1]
  • MATLAB, SPIDER, EMAN [1]
  • MOTIONCORR, IMOD, TOMOCTF, PEET, BSOFT [1]
  • MRC [1]
  • PHASER [1]
  • POINTLESS [1]
  • PROTOMO [1]
  • RELION, IHRSR [1]
  • ROTAN, FREALIGN [1]
  • SITUS [1]
  • SPIDER, EMAN, IHRSR, BSOFT [1]
  • SPIDER, EMAN1, EMAN2 [1]
  • SPIDER, IMAGIC-5, CTFFIND3, RELION [1]
  • SUPRIM, PHOELIX, IHRSR, SPIDER, CTFFIND3, CUSTOM, EMGLUE.PY [1]
  • UCSF CHIMERA, FLEX-EM [1]
  • XMIPP AND EMAN [1]
  • XSCALE [1]

Microscope

  • FEI TITAN KRIOS [360]
  • TFS KRIOS [111]
  • ZEISS LIBRA120PLUS [83]
  • FEI TECNAI F20 [44]
  • FEI POLARA 300 [25]
  • FEI TECNAI 20 [15]
  • JEOL 3200FSC [14]
  • FEI TITAN [13]
  • FEI TECNAI F30 [12]
  • JEOL 2200FS [11]
  • FEI TECNAI 12 [7]
  • FEI TALOS ARCTICA [6]
  • JEOL CRYO ARM 300 [5]
  • JEOL 2100 [4]
  • JEOL 4000EX [4]
  • TFS TALOS [4]
  • FEI/PHILIPS CM200FEG [3]
  • TFS GLACIOS [3]
  • FEI TECNAI ARCTICA [2]
  • FEI/PHILIPS CM300FEG/T [1]
  • JEOL 2000EX [1]

Electron Source

  • FIELD EMISSION GUN [621]
  • LAB6 [95]
  • TUNGSTEN HAIRPIN [5]
  • OTHER [4]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [197]
  • GATAN K3 6K X 4K [122]
  • GATAN ULTRASCAN 4000 4K X 4K [111]
  • GATAN K3 BIOQUANTUM 6K X 4K [90]
  • GATAN K2 QUANTUM 4K X 4K [41]
  • KODAK SO-163 FILM [27]
  • FEI FALCON III 4K X 4K [19]
  • FEI FALCON IV 4K X 4K [18]
  • OTHER [15]
  • FEI FALCON II 4K X 4K [14]
  • GATAN K2 BASE 4K X 4K [10]
  • FEI EAGLE 4K X 4K [8]
  • TVIPS TEMCAM-F416 4K X 4K [8]
  • DIRECT ELECTRON DE-20 5K X 3K [7]
  • TFS FALCON 4I 4K X 4K [6]
  • FEI FALCON I 4K X 4K [5]
  • DECTRIS ARINA 0.2K X 0.2K [4]
  • GENERIC CCD [4]
  • DIRECT ELECTRON DE-12 4K X 3K [3]
  • GATAN K2 4K X 4K [3]
  • TVIPS TEMCAM-F224 2K X 2K [3]
  • TVIPS TEMCAM-F415 4K X 4K [3]
  • GATAN ORIUS SC200 2K X 2K [2]
  • GATAN ULTRASCAN 1000 2K X 2K [2]
  • GATAN K3 BIOCONTINUUM 6K X 4K [1]
  • GENERIC GATAN 4K X 4K [1]

External links

  • PDB [278]
  • UniProt [271]
  • AlphaFold DB [246]
  • PDBe-Kb [220]
  • InterPro [219]
  • Gene Ontology [194]
  • ChEBI [171]
  • Pfam [163]
  • DrugBank [162]
  • ChEMBL [144]
  • EMPIAR [79]
  • Complex Portal [59]
  • SCOP2 [8]
  • CATH [3]