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subtomogram_extraction_software:"PyTom"

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Current Database

  • EMDB [127]

Current status

  • REL [127]

Sample type

  • Complex [60]
  • Cell [44]
  • Protein [22]
  • Cellular component [21]
  • RNA [10]
  • Ligand [5]
  • Virus [2]

Organism

  • Homo sapiens [41]
  • Mycoplasma pneumoniae [31]
  • Chlamydomonas reinhardtii [24]
  • Rattus norvegicus [5]
  • Synechocystis sp. pcc 6803 [4]
  • Saccharomyces cerevisiae [4]
  • Caenorhabditis elegans [4]
  • (no species) [2]
  • Methanococcus maripaludis [2]
  • Myxococcus xanthus [2]
  • Saccharomyces cerevisiae [2]
  • Oryctolagus cuniculus [2]
  • Orthoflavivirus encephalitidis [1]
  • Influenza a virus [1]
  • Human immunodeficiency virus 1 [1]
  • Schizosaccharomyces pombe [1]
  • Canis lupus [1]

EM Method

  • Subtomogram averaging [127]

Resolution

  • ≥ 2Å and < 3Å [1]
  • ≥ 3Å and < 4Å [5]
  • ≥ 4Å and < 5Å [12]
  • ≥ 5Å and < 6Å [7]
  • ≥ 6Å and < 8Å [19]
  • ≥ 8Å and < 12Å [26]
  • ≥ 12Å and < 16Å [14]
  • ≥ 16Å and < 20Å [9]
  • ≥ 20Å and < 30Å [15]
  • ≥ 30Å [19]

Model molecular weight

  • 250-500 kDa [1]
  • 1-2 MDa [4]
  • 2-5 MDa [13]

Release Date

  • 2026 [12]
  • 2025 [21]
  • 2024 [17]
  • 2022 [35]
  • 2019 [10]
  • 2018 [21]
  • 2017 [11]

Author by name

  • Engel BD [36]
  • Pfeffer S [36]
  • Mahamid J [35]
  • Forster F [32]
  • Xue L [31]
  • Kotecha A [28]
  • Plitzko JM [28]
  • Schaffer M [22]
  • Albanese P [20]
  • Baumeister W [20]
  • Beck F [20]
  • Chaillet ML [20]
  • Cuevas Arenas R [20]
  • Fedry J [20]
  • Forster FG [20]
  • Gemmer M [20]
  • Grollers-mulderij M [20]
  • Howes SC [20]
  • Koh FA [20]
  • Scheltema RA [20]
  • Vismpas D [20]
  • Van Loenhout J [20]
  • Albert S [17]
  • Schacherl M [16]
  • Spahn CMT [16]
  • Bork P [15]
  • Cramer P [15]
  • Lenz S [15]
  • Rappsilber J [15]
  • Tegunov D [15]
  • Zimmermann-kogadeeva M [15]
  • Spahn C [14]
  • Waltz F [14]
  • Foerster F [12]
  • Becker T [10]
  • Beckmann R [10]
  • Berninghausen O [10]
  • Braunger K [10]
  • Gilmore R [10]
  • Mandon EC [10]
  • Shrimal S [10]
  • Plitzko J [9]
  • Kelley R [8]
  • Khavnekar S [8]
  • Lamm L [8]
  • Obr M [8]
  • Righetto RD [8]
  • Van Der Stappen P [8]
  • Wietrzynski W [8]
  • Zhang X [8]
  • Asano S [7]
  • Beck M [7]
  • Filbeck S [7]
  • Gao Q [7]
  • Gruss OJ [7]
  • Hofer FW [7]
  • Kaplan C [7]
  • Mosalaganti S [7]
  • Neuner A [7]
  • Sala C [7]
  • Schiebel E [7]
  • Shin H [7]
  • Thomas HF [7]
  • Vermeulen BJA [7]
  • Wurtz M [7]
  • Zezlina M [7]
  • Guo Q [6]
  • Kater L [6]
  • Lehner PA [6]
  • Martinez-sanchez A [6]
  • Righetto R [6]
  • Salinas-giege T [6]
  • Wan W [6]
  • Edbauer D [5]
  • Fernandez-busnadiego R [5]
  • Frottin F [5]
  • Hartl FU [5]
  • Hartmann H [5]
  • Hipp MS [5]
  • Lehmer C [5]
  • Perez-berlanga M [5]
  • Rudack T [5]
  • Brittingham GP [4]
  • Chung JK [4]
  • Delarue M [4]
  • Fukuda Y [4]
  • Grotjahn DA [4]
  • Groves JT [4]
  • Gutierrez JI [4]
  • Holt LJ [4]
  • Jacobs-wagner C [4]
  • Kennedy KJ [4]
  • Kleindiek S [4]
  • Laugks T [4]
  • Lee C-W [4]
  • Nickelsen J [4]
  • Pinglay S [4]
  • Poterewicz G [4]
  • Rahmani H [4]
  • Rast A [4]

Author by ORCID

  • Pfeffer S [36]
  • Mahamid J [35]
  • Engel BD [32]
  • Forster F [32]
  • Xue L [31]
  • Kotecha A [26]
  • Chaillet ML [20]
  • Albanese P [20]
  • Scheltema RA [20]
  • Cuevas Arenas R [20]
  • Plitzko JM [20]
  • Fedry J [20]
  • Spahn CMT [16]
  • Schacherl M [16]
  • Cramer P [15]
  • Rappsilber J [15]
  • Zimmermann-kogadeeva M [15]
  • Bork P [15]
  • Lenz S [15]
  • Schaffer M [12]
  • Waltz F [12]
  • Becker T [10]
  • Mandon EC [10]
  • Gilmore R [10]
  • Shrimal S [10]
  • Braunger K [10]
  • Berninghausen O [10]
  • Beckmann R [10]
  • Khavnekar S [8]
  • Van Der Stappen P [8]
  • Filbeck S [7]
  • Gruss OJ [7]
  • Schiebel E [7]
  • Wurtz M [7]
  • Hofer FW [7]
  • Vermeulen BJA [7]
  • Gao Q [7]
  • Sala C [7]
  • Lehner PA [6]
  • Martinez-sanchez A [6]
  • Salinas-giege T [6]
  • Lamm L [6]
  • Obr M [6]
  • Guo Q [6]
  • Zhang X [6]
  • Righetto RD [6]
  • Kelley R [6]
  • Hipp MS [5]
  • Frottin F [5]
  • Edbauer D [5]
  • Fernandez-busnadiego R [5]
  • Grotjahn DA [4]
  • Holt LJ [4]
  • Pinglay S [4]
  • Rahmani H [4]
  • Jacobs-wagner C [4]
  • Wan W [4]
  • Nickelsen J [4]
  • Poterewicz G [4]
  • Thomas HF [3]
  • Mosalaganti S [3]
  • Herzik MA [2]
  • Narehood SM [2]
  • Westmeyer GG [2]
  • Kurumizaka H [2]
  • Kikkawa M [2]
  • Erdmann P [2]
  • Enos SE [2]
  • Bricault S [2]
  • Bachochin MJ [2]
  • Barad BA [2]
  • Heck AJR [2]
  • Sigmund F [2]
  • Kuschnerus IC [2]
  • Fuchs H [2]
  • Hatazawa S [2]
  • Cook BD [2]
  • Plitzko J [2]
  • Hrabe De Angelis M [2]
  • Lee CW [2]
  • Schuller JM [2]
  • Ntziachristos V [2]
  • Zid BM [2]
  • Fukuda Y [2]
  • Chang YT [2]
  • Salome PA [2]
  • Li Y [2]
  • Redford TH [2]
  • Dukakis P [2]
  • Ji D [2]
  • Hamid J [2]
  • Cartwright HN [1]
  • Wingreen NS [1]
  • Cherepanov P [1]
  • Strauss M [1]
  • Lin J [1]
  • Ji W [1]
  • Cook NJ [1]
  • So-last MGF [1]
  • Nans A [1]

Journal

  • NATURE [38]
  • BIORXIV [26]
  • NAT STRUCT MOL BIOL [16]
  • SCIENCE [16]
  • PNAS [11]
  • CELL [10]
  • NAT COMMUN [9]
  • TO BE PUBLISHED [8]
  • NAT METHODS [5]
  • NAT PLANTS [4]
  • GENES CELLS [2]
  • J CELL BIOL [2]
  • MOL CELL [2]
  • SCI ADV [1]
  • STRUCTURE [1]

Software

  • PYTOM [127]
  • RELION [107]
  • WARP [49]
  • CTFFIND [11]
  • IMOD [10]
  • STOPGAP [7]
  • ARETOMO [6]
  • TOM TOOLBOX [6]
  • M [4]
  • AMIRA [1]
  • AV3 [1]

Microscope

  • FEI TITAN KRIOS [70]
  • TFS KRIOS [34]
  • FEI TALOS ARCTICA [20]
  • FEI POLARA 300 [3]

Electron Source

  • FIELD EMISSION GUN [127]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [77]
  • GATAN K3 BIOQUANTUM 6K X 4K [25]
  • TFS FALCON 4I 4K X 4K [17]
  • GATAN K3 6K X 4K [5]
  • FEI FALCON IV 4K X 4K [3]

External links

  • PDB [127]
  • EMPIAR [23]
  • PDBe-Kb [20]
  • UniProt [20]
  • AlphaFold DB [19]
  • Gene Ontology [18]
  • InterPro [18]
  • Pfam [18]
  • SCOP2 [7]
  • Complex Portal [6]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [5]
Sort by: Download
Showing 1 - 10 of 127. Page 1 of 13
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EMD-58187
Download Map
3D View
Subtomogram average of human Hsp60-Hsp10 from EMPIAR-13145
CryoEM
Release date: June 3, 2026
Resolution: 8.0 Å
EM Method: Subtomogram averaging

So-Last MGF, Hale T, Burt A, Allegretti MA

To Be Published

EMD-58201
Download Map
3D View
In situ subtomogram average of the M. maripaludis Hdr-Vhu-Fwd supercomplex
CryoEM
Release date: June 3, 2026
Resolution: 11.1 Å
EM Method: Subtomogram averaging

Paul S, Pascoa TC, Klamke MA, Bohn S, Abendroth F, Deobald D, Vasquez O, Stripp ST, Schuller JM

To Be Published

EMD-58202
Download Map
3D View
In situ subtomogram average of the M. maripaludis 70S ribosome
CryoEM
Release date: June 3, 2026
Resolution: 4.07 Å
EM Method: Subtomogram averaging

Paul S, Pascoa TC, Klamke MA, Bohn S, Abendroth F, Deobald D, Vasquez O, Stripp ST, Schuller JM

To Be Published

EMD-55312
Download Map
3D View
Immature TBEV envelope spike with interaction partners underneath - STA
CryoEM
Release date: May 20, 2026
Resolution: 4.24 Å
EM Method: Subtomogram averaging

Fuzik T, Anastasina M, Pajtinka P, Domanska A, Pulkkinen LIA, Smerdova L, Nepovimova L, Formanova-Pokorna P, Strakova P, Novacek J, Ruzek D, Vacha R, Butcher SJ, Plevka P

To Be Published

EMD-75902
Download Map
3D View
Influenza A virus Hemagglutinin A/Darwin/6/2021 H3N2 C3 symmetry; subtomogram averaged determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT
CryoEM
Release date: April 8, 2026
Resolution: 7.5 Å
EM Method: Subtomogram averaging

Enos SE, Cook BD, Rahmani H, Narehood SM, Li Y, Kuschnerus IC, Redford TH, Dukakis P, Ji D, Bachochin MJ, Grotjahn DA, Herzik MA

bioRxiv (2026) [ DOI: doi:10.64898/2026.03.17.712260 Pubmed: 41889805 ]

EMD-75904
Download Map
3D View
Rabbit muscle Aldolase C1 symmetry; subtomogram averaged determined using the SPT Labtech chameleon in the presence of 0.25x SurfACT
CryoEM
Release date: April 8, 2026
Resolution: 8.8 Å
EM Method: Subtomogram averaging

Enos SE, Cook BD, Rahmani H, Narehood SM, Li Y, Kuschnerus IC, Redford TH, Dukakis P, Ji D, Bachochin MJ, Grotjahn DA, Herzik MA

bioRxiv (2026) [ DOI: doi:10.64898/2026.03.17.712260 Pubmed: 41889805 ]

EMD-56139
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3D View
Subtomogram average of the Chlamydomonas reinhardtii chlororibosome - consensus map
Consensus map
CryoEM
Release date: Feb. 18, 2026
Resolution: 6.11 Å
EM Method: Subtomogram averaging

Waltz F, Lehner PA, Van der Stappen P, Kater L, Pfeffer S, Engel BD

bioRxiv (2026) [ DOI: doi:10.64898/2026.02.07.704542 Pubmed: 41727112 ]

EMD-56140
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3D View
Subtomogram average of the Chlamydomonas reinhardtii chlororibosome - LSU focused
Focused map
CryoEM
Release date: Feb. 18, 2026
Resolution: 5.76 Å
EM Method: Subtomogram averaging

Waltz F, Lehner PA, Van der Stappen P, Kater L, Pfeffer S, Engel BD

bioRxiv (2026) [ DOI: doi:10.64898/2026.02.07.704542 Pubmed: 41727112 ]

EMD-56141
Download Map
3D View
Subtomogram average of the Chlamydomonas reinhardtii chlororibosome - SSU focused
Focused map
CryoEM
Release date: Feb. 18, 2026
Resolution: 6.36 Å
EM Method: Subtomogram averaging

Waltz F, Lehner PA, Van der Stappen P, Kater L, Pfeffer S, Engel BD

bioRxiv (2026) [ DOI: doi:10.64898/2026.02.07.704542 Pubmed: 41727112 ]

EMD-56142
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3D View
Subtomogram average of the Chlamydomonas reinhardtii chlororibosome - SSU extension focused
Focused map
CryoEM
Release date: Feb. 18, 2026
Resolution: 8.48 Å
EM Method: Subtomogram averaging

Waltz F, Lehner PA, Van der Stappen P, Kater L, Pfeffer S, Engel BD

bioRxiv (2026) [ DOI: doi:10.64898/2026.02.07.704542 Pubmed: 41727112 ]

Sort by: Download
Showing 1 - 10 of 127. Page 1 of 13
Display:
Statistics
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Preview first 10
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Filter By

Current Database

  • EMDB [127]

Current status

  • REL [127]

Sample type

  • Complex [60]
  • Cell [44]
  • Protein [22]
  • Cellular component [21]
  • RNA [10]
  • Ligand [5]
  • Virus [2]

Organism

  • Homo sapiens [41]
  • Mycoplasma pneumoniae [31]
  • Chlamydomonas reinhardtii [24]
  • Rattus norvegicus [5]
  • Synechocystis sp. pcc 6803 [4]
  • Saccharomyces cerevisiae [4]
  • Caenorhabditis elegans [4]
  • (no species) [2]
  • Methanococcus maripaludis [2]
  • Myxococcus xanthus [2]
  • Saccharomyces cerevisiae [2]
  • Oryctolagus cuniculus [2]
  • Orthoflavivirus encephalitidis [1]
  • Influenza a virus [1]
  • Human immunodeficiency virus 1 [1]
  • Schizosaccharomyces pombe [1]
  • Canis lupus [1]

EM Method

  • Subtomogram averaging [127]

Resolution

  • ≥ 2Å and < 3Å [1]
  • ≥ 3Å and < 4Å [5]
  • ≥ 4Å and < 5Å [12]
  • ≥ 5Å and < 6Å [7]
  • ≥ 6Å and < 8Å [19]
  • ≥ 8Å and < 12Å [26]
  • ≥ 12Å and < 16Å [14]
  • ≥ 16Å and < 20Å [9]
  • ≥ 20Å and < 30Å [15]
  • ≥ 30Å [19]

Model molecular weight

  • 250-500 kDa [1]
  • 1-2 MDa [4]
  • 2-5 MDa [13]

Release Date

  • 2026 [12]
  • 2025 [21]
  • 2024 [17]
  • 2022 [35]
  • 2019 [10]
  • 2018 [21]
  • 2017 [11]

Author by name

  • Engel BD [36]
  • Pfeffer S [36]
  • Mahamid J [35]
  • Forster F [32]
  • Xue L [31]
  • Kotecha A [28]
  • Plitzko JM [28]
  • Schaffer M [22]
  • Albanese P [20]
  • Baumeister W [20]
  • Beck F [20]
  • Chaillet ML [20]
  • Cuevas Arenas R [20]
  • Fedry J [20]
  • Forster FG [20]
  • Gemmer M [20]
  • Grollers-mulderij M [20]
  • Howes SC [20]
  • Koh FA [20]
  • Scheltema RA [20]
  • Vismpas D [20]
  • Van Loenhout J [20]
  • Albert S [17]
  • Schacherl M [16]
  • Spahn CMT [16]
  • Bork P [15]
  • Cramer P [15]
  • Lenz S [15]
  • Rappsilber J [15]
  • Tegunov D [15]
  • Zimmermann-kogadeeva M [15]
  • Spahn C [14]
  • Waltz F [14]
  • Foerster F [12]
  • Becker T [10]
  • Beckmann R [10]
  • Berninghausen O [10]
  • Braunger K [10]
  • Gilmore R [10]
  • Mandon EC [10]
  • Shrimal S [10]
  • Plitzko J [9]
  • Kelley R [8]
  • Khavnekar S [8]
  • Lamm L [8]
  • Obr M [8]
  • Righetto RD [8]
  • Van Der Stappen P [8]
  • Wietrzynski W [8]
  • Zhang X [8]
  • Asano S [7]
  • Beck M [7]
  • Filbeck S [7]
  • Gao Q [7]
  • Gruss OJ [7]
  • Hofer FW [7]
  • Kaplan C [7]
  • Mosalaganti S [7]
  • Neuner A [7]
  • Sala C [7]
  • Schiebel E [7]
  • Shin H [7]
  • Thomas HF [7]
  • Vermeulen BJA [7]
  • Wurtz M [7]
  • Zezlina M [7]
  • Guo Q [6]
  • Kater L [6]
  • Lehner PA [6]
  • Martinez-sanchez A [6]
  • Righetto R [6]
  • Salinas-giege T [6]
  • Wan W [6]
  • Edbauer D [5]
  • Fernandez-busnadiego R [5]
  • Frottin F [5]
  • Hartl FU [5]
  • Hartmann H [5]
  • Hipp MS [5]
  • Lehmer C [5]
  • Perez-berlanga M [5]
  • Rudack T [5]
  • Brittingham GP [4]
  • Chung JK [4]
  • Delarue M [4]
  • Fukuda Y [4]
  • Grotjahn DA [4]
  • Groves JT [4]
  • Gutierrez JI [4]
  • Holt LJ [4]
  • Jacobs-wagner C [4]
  • Kennedy KJ [4]
  • Kleindiek S [4]
  • Laugks T [4]
  • Lee C-W [4]
  • Nickelsen J [4]
  • Pinglay S [4]
  • Poterewicz G [4]
  • Rahmani H [4]
  • Rast A [4]

Author by ORCID

  • Pfeffer S [36]
  • Mahamid J [35]
  • Engel BD [32]
  • Forster F [32]
  • Xue L [31]
  • Kotecha A [26]
  • Chaillet ML [20]
  • Albanese P [20]
  • Scheltema RA [20]
  • Cuevas Arenas R [20]
  • Plitzko JM [20]
  • Fedry J [20]
  • Spahn CMT [16]
  • Schacherl M [16]
  • Cramer P [15]
  • Rappsilber J [15]
  • Zimmermann-kogadeeva M [15]
  • Bork P [15]
  • Lenz S [15]
  • Schaffer M [12]
  • Waltz F [12]
  • Becker T [10]
  • Mandon EC [10]
  • Gilmore R [10]
  • Shrimal S [10]
  • Braunger K [10]
  • Berninghausen O [10]
  • Beckmann R [10]
  • Khavnekar S [8]
  • Van Der Stappen P [8]
  • Filbeck S [7]
  • Gruss OJ [7]
  • Schiebel E [7]
  • Wurtz M [7]
  • Hofer FW [7]
  • Vermeulen BJA [7]
  • Gao Q [7]
  • Sala C [7]
  • Lehner PA [6]
  • Martinez-sanchez A [6]
  • Salinas-giege T [6]
  • Lamm L [6]
  • Obr M [6]
  • Guo Q [6]
  • Zhang X [6]
  • Righetto RD [6]
  • Kelley R [6]
  • Hipp MS [5]
  • Frottin F [5]
  • Edbauer D [5]
  • Fernandez-busnadiego R [5]
  • Grotjahn DA [4]
  • Holt LJ [4]
  • Pinglay S [4]
  • Rahmani H [4]
  • Jacobs-wagner C [4]
  • Wan W [4]
  • Nickelsen J [4]
  • Poterewicz G [4]
  • Thomas HF [3]
  • Mosalaganti S [3]
  • Herzik MA [2]
  • Narehood SM [2]
  • Westmeyer GG [2]
  • Kurumizaka H [2]
  • Kikkawa M [2]
  • Erdmann P [2]
  • Enos SE [2]
  • Bricault S [2]
  • Bachochin MJ [2]
  • Barad BA [2]
  • Heck AJR [2]
  • Sigmund F [2]
  • Kuschnerus IC [2]
  • Fuchs H [2]
  • Hatazawa S [2]
  • Cook BD [2]
  • Plitzko J [2]
  • Hrabe De Angelis M [2]
  • Lee CW [2]
  • Schuller JM [2]
  • Ntziachristos V [2]
  • Zid BM [2]
  • Fukuda Y [2]
  • Chang YT [2]
  • Salome PA [2]
  • Li Y [2]
  • Redford TH [2]
  • Dukakis P [2]
  • Ji D [2]
  • Hamid J [2]
  • Cartwright HN [1]
  • Wingreen NS [1]
  • Cherepanov P [1]
  • Strauss M [1]
  • Lin J [1]
  • Ji W [1]
  • Cook NJ [1]
  • So-last MGF [1]
  • Nans A [1]

Journal

  • NATURE [38]
  • BIORXIV [26]
  • NAT STRUCT MOL BIOL [16]
  • SCIENCE [16]
  • PNAS [11]
  • CELL [10]
  • NAT COMMUN [9]
  • TO BE PUBLISHED [8]
  • NAT METHODS [5]
  • NAT PLANTS [4]
  • GENES CELLS [2]
  • J CELL BIOL [2]
  • MOL CELL [2]
  • SCI ADV [1]
  • STRUCTURE [1]

Software

  • PYTOM [127]
  • RELION [107]
  • WARP [49]
  • CTFFIND [11]
  • IMOD [10]
  • STOPGAP [7]
  • ARETOMO [6]
  • TOM TOOLBOX [6]
  • M [4]
  • AMIRA [1]
  • AV3 [1]

Microscope

  • FEI TITAN KRIOS [70]
  • TFS KRIOS [34]
  • FEI TALOS ARCTICA [20]
  • FEI POLARA 300 [3]

Electron Source

  • FIELD EMISSION GUN [127]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [77]
  • GATAN K3 BIOQUANTUM 6K X 4K [25]
  • TFS FALCON 4I 4K X 4K [17]
  • GATAN K3 6K X 4K [5]
  • FEI FALCON IV 4K X 4K [3]

External links

  • PDB [127]
  • EMPIAR [23]
  • PDBe-Kb [20]
  • UniProt [20]
  • AlphaFold DB [19]
  • Gene Ontology [18]
  • InterPro [18]
  • Pfam [18]
  • SCOP2 [7]
  • Complex Portal [6]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [5]