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Current Database

  • EMDB [712]

Current status

  • REL [712]

Sample type

  • Complex [431]
  • Protein [305]
  • Ligand [178]
  • Cell [101]
  • Sample [83]
  • Virus [74]
  • Cellular component [71]
  • RNA [38]
  • DNA [36]
  • Tissue [8]
  • Other [4]

Organism

  • Homo sapiens [178]
  • Mus musculus [46]
  • Escherichia coli [33]
  • 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]
  • Streptomyces coelicolor [3]
  • Rattus rattus [3]
  • Paramecium bursaria chlorella virus 1 [3]
  • Salmonella phage p22 [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]
  • Bacillus subtilis [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]
  • Xenopus laevis [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]
  • Nudaurelia capensis omega virus [1]
  • Escherichia coli [1]
  • Streptococcus pneumoniae [1]

EM Method

  • Single-particle [325]
  • Tomography [273]
  • Subtomogram averaging [62]
  • Helical reconstruction [43]
  • Electron Crystallography [9]

Resolution

  • < 2Å [2]
  • ≥ 2Å and < 3Å [68]
  • ≥ 3Å and < 4Å [163]
  • ≥ 4Å and < 5Å [43]
  • ≥ 5Å and < 6Å [11]
  • ≥ 6Å and < 8Å [18]
  • ≥ 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 [12]
  • 100-250 kDa [135]
  • 250-500 kDa [54]
  • 500-1000 kDa [22]
  • 1-2 MDa [11]
  • 2-5 MDa [7]
  • 5-10 MDa [8]
  • > 10 MDa [3]

Release Date

  • 2026 [34]
  • 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 [59]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Hirano H [33]
  • Omura SN [31]
  • Nakagawa R [26]
  • Moores CA [21]
  • Sano FK [21]
  • Weiss GL [19]
  • Mahamid J [18]
  • Yamashita K [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]
  • Zhang J [11]
  • Ishiguro S [10]
  • Major J [10]
  • Ohmori T [10]
  • Rosenfeld SS [10]
  • Su CC [10]
  • Yachie N [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 K [9]
  • Lin C-W [9]
  • Lin CW [9]
  • Maldener I [9]
  • Mori H [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]
  • Feng Z [8]
  • Fu C [8]
  • Gadadhar S [8]

Author by ORCID

  • Ren G [82]
  • Lei M [80]
  • Nureki O [53]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Omura SN [31]
  • Sano FK [21]
  • Moores CA [20]
  • Weiss GL [19]
  • Mahamid J [18]
  • Kusakizako T [17]
  • Tanaka T [15]
  • Yamashita K [15]
  • Chiu W [14]
  • Zhang F [14]
  • Zuckerman DM [13]
  • Driggers CM [13]
  • Pigino G [13]
  • Russo JD [13]
  • Shihoya W [13]
  • Shuto Y [13]
  • Goulet A [12]
  • Yu EW [11]
  • Elbaum M [11]
  • Grigorieff N [11]
  • Schmid MF [11]
  • Ohmori T [10]
  • Zyla DS [9]
  • Li S [9]
  • Truck J [9]
  • Feldmuller M [9]
  • Stanisich JJ [9]
  • Okamoto HH [9]
  • Gaubitz C [9]
  • Liu X [9]
  • Sauer MM [9]
  • Aebi M [9]
  • Akasaka H [9]
  • Glockshuber R [9]
  • Agard DA [9]
  • Devuyst O [9]
  • Lin CW [9]
  • Toure A [8]
  • Gong A [8]
  • Janke C [8]
  • Baldus M [8]
  • Whitfield M [8]
  • Ziyyat A [8]
  • Leboucher S [8]
  • Hansen JN [8]
  • Alvarez L [8]
  • Hora M [8]
  • Feng Z [8]
  • Neumann M [8]
  • Accardi A [8]
  • Boehringer D [8]
  • Beck M [8]
  • Chlanda P [8]
  • Topf M [8]
  • Kostarev A [8]
  • Leitner A [8]
  • Gadadhar S [8]
  • Bieri P [7]
  • Ludtke SJ [7]
  • Nishimasu H [7]
  • Grunewald K [7]
  • Siebert CA [7]
  • Marshall WF [7]
  • Dogterom M [7]
  • Rubinstein JL [7]
  • Kashiwakura Y [7]
  • Fernandez JJ [7]
  • Hoffmann PC [7]
  • Villa E [7]
  • Bose M [6]
  • Pajak J [6]
  • Thibaut HJ [6]
  • Van Kuppeveld Fjm [6]
  • Lyoo H [6]
  • Ivica J [6]
  • Tsai SQ [6]
  • Baker TA [6]
  • Stahlberg H [6]
  • Eisenstein F [6]
  • Baggen J [6]
  • Sauer RT [6]
  • Kuhlbrandt W [6]
  • Kukulski W [6]
  • Ishiguro S [6]
  • Ericson CF [6]
  • Kobayashi K [6]
  • Schellenberger P [6]
  • Lampe M [6]
  • Ephrussi A [6]
  • Amunts A [6]
  • Demo G [6]
  • Stone NP [6]
  • Baradaran R [6]
  • Atherton J [6]
  • Greger IH [6]

Journal

  • NAT COMMUN [107]
  • SCI REP [83]
  • ELIFE [63]
  • PNAS [56]
  • SCIENCE [42]
  • NAT STRUCT MOL BIOL [37]
  • BIORXIV [35]
  • CELL [35]
  • NATURE [34]
  • TO BE PUBLISHED [29]
  • STRUCTURE [25]
  • J MOL BIOL [21]
  • COMMUN BIOL [14]
  • NAT MICROBIOL [13]
  • J VIROL [11]
  • MBIO [11]
  • MOL CELL [11]
  • SCI ADV [10]
  • NAT CELL BIOL [7]
  • EMBO J [6]
  • 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 [126]
  • IMOD [104]
  • CRYOSPARC [55]
  • CTFFIND [25]
  • CHIMERA [17]
  • EMAN2 [14]
  • GCTF [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]
  • 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]
  • WARP [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 [100]
  • 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]
  • JEOL CRYO ARM 300 [5]
  • FEI TALOS ARCTICA [4]
  • 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 [608]
  • LAB6 [95]
  • TUNGSTEN HAIRPIN [5]
  • OTHER [4]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [195]
  • GATAN K3 6K X 4K [120]
  • GATAN ULTRASCAN 4000 4K X 4K [111]
  • GATAN K3 BIOQUANTUM 6K X 4K [83]
  • 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 [17]
  • OTHER [15]
  • FEI FALCON II 4K X 4K [14]
  • GATAN K2 BASE 4K X 4K [9]
  • 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 [712]
  • UniProt [266]
  • PDBe-Kb [242]
  • AlphaFold DB [241]
  • InterPro [220]
  • Gene Ontology [190]
  • ChEBI [163]
  • Pfam [158]
  • DrugBank [154]
  • ChEMBL [136]
  • EMPIAR [77]
  • Complex Portal [58]
  • SCOP2 [9]
  • CATH [3]
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EMD-72772
Download Map
3D View
Structure of the Adenovirus-7 VLP, Class 4
CryoEM
Release date: July 1, 2026
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 9ych
Q-score: 0.547

Madoo K, Mazboudi R, Islam ZM, Luo J, Kuschner RA, Gottlieb P, Dennehy JJ, Abzalimov RR, Galarza JM, Khayat R

PNAS (2026) 123 pp. e2526969123-e2526969123 [ Pubmed: 42301791 DOI: doi:10.1073/pnas.2526969123 ]

EMD-72773
Download Map
3D View
Structure of the Adenovirus-7 VLP, Class 3
CryoEM
Release date: July 1, 2026
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9yci
Q-score: 0.531

Madoo K, Mazboudi R, Islam ZM, Luo J, Kuschner RA, Gottlieb P, Dennehy JJ, Abzalimov RR, Galarza JM, Khayat R

PNAS (2026) 123 pp. e2526969123-e2526969123 [ Pubmed: 42301791 DOI: doi:10.1073/pnas.2526969123 ]

EMD-72774
Download Map
3D View
Structure of the Adenovirus-7 VLP, Class 2
CryoEM
Release date: July 1, 2026
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 9ycj
Q-score: 0.498

Madoo K, Mazboudi R, Islam ZM, Luo J, Kuschner RA, Gottlieb P, Dennehy JJ, Abzalimov RR, Galarza JM, Khayat R

PNAS (2026) 123 pp. e2526969123-e2526969123 [ Pubmed: 42301791 DOI: doi:10.1073/pnas.2526969123 ]

EMD-72793
Download Map
3D View
Structure of the Adenovirus-7 VLP, Class 1
CryoEM
Release date: July 1, 2026
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9yd0
Q-score: 0.536

Madoo K, Mazboudi R, Islam ZM, Luo J, Kuschner RA, Gottlieb P, Dennehy JJ, Abzalimov RR, Galarza JM, Khayat R

PNAS (2026) 123 pp. e2526969123-e2526969123 [ Pubmed: 42301791 DOI: doi:10.1073/pnas.2526969123 ]

EMD-57915
Download Map
3D View
Siphohage OE33PA upon binding to its Gram host cell surface view 1
CryoEM
Release date: June 17, 2026
EM Method: Tomography

Schmitt L, Chaib A, Ptchelkine D, Kandiah E, Le Marrec C, Cambillau C, Goulet A

bioRxiv (2026) [ DOI: doi:10.64898/2026.05.20.726473 Pubmed: 42244550 ]

EMD-57918
Download Map
3D View
Siphohage OE33PA upon binding to its Gram host cell surface view 3
CryoEM
Release date: June 17, 2026
EM Method: Tomography

Schmitt L, Chaib A, Ptchelkine D, Kandiah E, Le Marrec C, Cambillau C, Goulet A

bioRxiv (2026) [ DOI: doi:10.64898/2026.05.20.726473 Pubmed: 42244550 ]

EMD-57919
Download Map
3D View
Siphohage OE33PA upon binding to its Gram host cell surface view 4
CryoEM
Release date: June 17, 2026
EM Method: Tomography

Schmitt L, Chaib A, Ptchelkine D, Kandiah E, Le Marrec C, Cambillau C, Goulet A

bioRxiv (2026) [ DOI: doi:10.64898/2026.05.20.726473 Pubmed: 42244550 ]

EMD-57920
Download Map
3D View
Siphohage OE33PA upon binding to its Gram host cell surface view 5
CryoEM
Release date: June 17, 2026
EM Method: Tomography

Schmitt L, Chaib A, Ptchelkine D, Kandiah E, Le Marrec C, Cambillau C, Goulet A

bioRxiv (2026) [ DOI: doi:10.64898/2026.05.20.726473 Pubmed: 42244550 ]

EMD-57922
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Siphohage OE33PA upon binding to its Gram host cell surface view 7
CryoEM
Release date: June 17, 2026
EM Method: Tomography

Schmitt L, Chaib A, Ptchelkine D, Kandiah E, Le Marrec C, Cambillau C, Goulet A

bioRxiv (2026) [ DOI: doi:10.64898/2026.05.20.726473 Pubmed: 42244550 ]

EMD-58124
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In situ subtomogram average of a ribosome bound to ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen mNeon-KDEL
CryoEM
Release date: June 3, 2026
Resolution: 22.0 Å
EM Method: Subtomogram averaging

Martin-Solana E, Carter SD, Donahue EKF, Ning J, Glausier JR, Preisegger MA, Eisenman L, Joseph PN, Bouchet-Marquis C, Wu K, Mobini CL, Frantz AN, Puig S, Hampton CM, Kabbani N, Jensen GJ, Watkins SC, Deisseroth K, Fenno LE, Gold MS, Wills ZP, Burkewitz K, Das S, Freyberg Z

bioRxiv (2024) [ Pubmed: 38895376 DOI: doi:10.1101/2024.06.07.598007 ]

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Current Database

  • EMDB [712]

Current status

  • REL [712]

Sample type

  • Complex [431]
  • Protein [305]
  • Ligand [178]
  • Cell [101]
  • Sample [83]
  • Virus [74]
  • Cellular component [71]
  • RNA [38]
  • DNA [36]
  • Tissue [8]
  • Other [4]

Organism

  • Homo sapiens [178]
  • Mus musculus [46]
  • Escherichia coli [33]
  • 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]
  • Streptomyces coelicolor [3]
  • Rattus rattus [3]
  • Paramecium bursaria chlorella virus 1 [3]
  • Salmonella phage p22 [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]
  • Bacillus subtilis [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]
  • Xenopus laevis [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]
  • Nudaurelia capensis omega virus [1]
  • Escherichia coli [1]
  • Streptococcus pneumoniae [1]

EM Method

  • Single-particle [325]
  • Tomography [273]
  • Subtomogram averaging [62]
  • Helical reconstruction [43]
  • Electron Crystallography [9]

Resolution

  • < 2Å [2]
  • ≥ 2Å and < 3Å [68]
  • ≥ 3Å and < 4Å [163]
  • ≥ 4Å and < 5Å [43]
  • ≥ 5Å and < 6Å [11]
  • ≥ 6Å and < 8Å [18]
  • ≥ 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 [12]
  • 100-250 kDa [135]
  • 250-500 kDa [54]
  • 500-1000 kDa [22]
  • 1-2 MDa [11]
  • 2-5 MDa [7]
  • 5-10 MDa [8]
  • > 10 MDa [3]

Release Date

  • 2026 [34]
  • 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 [59]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Hirano H [33]
  • Omura SN [31]
  • Nakagawa R [26]
  • Moores CA [21]
  • Sano FK [21]
  • Weiss GL [19]
  • Mahamid J [18]
  • Yamashita K [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]
  • Zhang J [11]
  • Ishiguro S [10]
  • Major J [10]
  • Ohmori T [10]
  • Rosenfeld SS [10]
  • Su CC [10]
  • Yachie N [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 K [9]
  • Lin C-W [9]
  • Lin CW [9]
  • Maldener I [9]
  • Mori H [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]
  • Feng Z [8]
  • Fu C [8]
  • Gadadhar S [8]

Author by ORCID

  • Ren G [82]
  • Lei M [80]
  • Nureki O [53]
  • Pilhofer M [47]
  • Itoh Y [37]
  • Omura SN [31]
  • Sano FK [21]
  • Moores CA [20]
  • Weiss GL [19]
  • Mahamid J [18]
  • Kusakizako T [17]
  • Tanaka T [15]
  • Yamashita K [15]
  • Chiu W [14]
  • Zhang F [14]
  • Zuckerman DM [13]
  • Driggers CM [13]
  • Pigino G [13]
  • Russo JD [13]
  • Shihoya W [13]
  • Shuto Y [13]
  • Goulet A [12]
  • Yu EW [11]
  • Elbaum M [11]
  • Grigorieff N [11]
  • Schmid MF [11]
  • Ohmori T [10]
  • Zyla DS [9]
  • Li S [9]
  • Truck J [9]
  • Feldmuller M [9]
  • Stanisich JJ [9]
  • Okamoto HH [9]
  • Gaubitz C [9]
  • Liu X [9]
  • Sauer MM [9]
  • Aebi M [9]
  • Akasaka H [9]
  • Glockshuber R [9]
  • Agard DA [9]
  • Devuyst O [9]
  • Lin CW [9]
  • Toure A [8]
  • Gong A [8]
  • Janke C [8]
  • Baldus M [8]
  • Whitfield M [8]
  • Ziyyat A [8]
  • Leboucher S [8]
  • Hansen JN [8]
  • Alvarez L [8]
  • Hora M [8]
  • Feng Z [8]
  • Neumann M [8]
  • Accardi A [8]
  • Boehringer D [8]
  • Beck M [8]
  • Chlanda P [8]
  • Topf M [8]
  • Kostarev A [8]
  • Leitner A [8]
  • Gadadhar S [8]
  • Bieri P [7]
  • Ludtke SJ [7]
  • Nishimasu H [7]
  • Grunewald K [7]
  • Siebert CA [7]
  • Marshall WF [7]
  • Dogterom M [7]
  • Rubinstein JL [7]
  • Kashiwakura Y [7]
  • Fernandez JJ [7]
  • Hoffmann PC [7]
  • Villa E [7]
  • Bose M [6]
  • Pajak J [6]
  • Thibaut HJ [6]
  • Van Kuppeveld Fjm [6]
  • Lyoo H [6]
  • Ivica J [6]
  • Tsai SQ [6]
  • Baker TA [6]
  • Stahlberg H [6]
  • Eisenstein F [6]
  • Baggen J [6]
  • Sauer RT [6]
  • Kuhlbrandt W [6]
  • Kukulski W [6]
  • Ishiguro S [6]
  • Ericson CF [6]
  • Kobayashi K [6]
  • Schellenberger P [6]
  • Lampe M [6]
  • Ephrussi A [6]
  • Amunts A [6]
  • Demo G [6]
  • Stone NP [6]
  • Baradaran R [6]
  • Atherton J [6]
  • Greger IH [6]

Journal

  • NAT COMMUN [107]
  • SCI REP [83]
  • ELIFE [63]
  • PNAS [56]
  • SCIENCE [42]
  • NAT STRUCT MOL BIOL [37]
  • BIORXIV [35]
  • CELL [35]
  • NATURE [34]
  • TO BE PUBLISHED [29]
  • STRUCTURE [25]
  • J MOL BIOL [21]
  • COMMUN BIOL [14]
  • NAT MICROBIOL [13]
  • J VIROL [11]
  • MBIO [11]
  • MOL CELL [11]
  • SCI ADV [10]
  • NAT CELL BIOL [7]
  • EMBO J [6]
  • 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 [126]
  • IMOD [104]
  • CRYOSPARC [55]
  • CTFFIND [25]
  • CHIMERA [17]
  • EMAN2 [14]
  • GCTF [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]
  • 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]
  • WARP [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 [100]
  • 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]
  • JEOL CRYO ARM 300 [5]
  • FEI TALOS ARCTICA [4]
  • 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 [608]
  • LAB6 [95]
  • TUNGSTEN HAIRPIN [5]
  • OTHER [4]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [195]
  • GATAN K3 6K X 4K [120]
  • GATAN ULTRASCAN 4000 4K X 4K [111]
  • GATAN K3 BIOQUANTUM 6K X 4K [83]
  • 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 [17]
  • OTHER [15]
  • FEI FALCON II 4K X 4K [14]
  • GATAN K2 BASE 4K X 4K [9]
  • 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 [712]
  • UniProt [266]
  • PDBe-Kb [242]
  • AlphaFold DB [241]
  • InterPro [220]
  • Gene Ontology [190]
  • ChEBI [163]
  • Pfam [158]
  • DrugBank [154]
  • ChEMBL [136]
  • EMPIAR [77]
  • Complex Portal [58]
  • SCOP2 [9]
  • CATH [3]