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author:"Perilla JR"

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Current Database

  • EMDB [67]
  • EMPIAR [1]

Current status

  • REL [68]

Sample type

  • Virus [51]
  • Protein [48]
  • Ligand [14]
  • Complex [10]
  • Sample [7]
  • RNA [1]

Organism

  • Human immunodeficiency virus 1 [22]
  • Human immunodeficiency virus 1 [10]
  • Human immunodeficiency virus 1 [9]
  • Equine infectious anemia virus [6]
  • Human endogenous retrovirus k [4]
  • Human immunodeficiency virus 1 [3]
  • Escherichia coli [3]
  • Caprine arthritis encephalitis virus [2]
  • Simian immunodeficiency virus [2]
  • Primate t-lymphotropic virus 1 [2]
  • Visna-maedi virus [2]
  • Uncultured virus [2]
  • Equine infectious anemia virus [1]
  • Human immunodeficiency virus 1 [1]
  • Chlamydomonas reinhardtii [1]
  • Synthetic construct [1]
  • Homo sapiens [1]

EM Method

  • Subtomogram averaging [32]
  • Single-particle [25]
  • Helical reconstruction [6]
  • Tomography [4]

Resolution

  • ≥ 2Å and < 3Å [8]
  • ≥ 3Å and < 4Å [23]
  • ≥ 4Å and < 5Å [7]
  • ≥ 5Å and < 6Å [4]
  • ≥ 6Å and < 8Å [6]
  • ≥ 8Å and < 12Å [13]
  • ≥ 12Å and < 16Å [1]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 50-100 kDa [1]
  • 100-250 kDa [6]
  • 250-500 kDa [13]
  • 500-1000 kDa [6]
  • 1-2 MDa [1]
  • 2-5 MDa [1]
  • 5-10 MDa [1]
  • > 10 MDa [1]

Release Date

  • 2026 [6]
  • 2025 [28]
  • 2024 [7]
  • 2023 [1]
  • 2021 [10]
  • 2020 [6]
  • 2018 [1]
  • 2017 [2]
  • 2016 [2]
  • 2015 [3]
  • 2013 [2]

Author by name

  • Perilla JR [67]
  • Zhang P [44]
  • Rey JS [35]
  • Zhu Y [24]
  • Shen Y [17]
  • Xu C [16]
  • Freed EO [15]
  • Ning J [15]
  • Ahn J [14]
  • Aiken C [14]
  • Chen L [14]
  • Freniere C [14]
  • Wu C [14]
  • Xiong Y [14]
  • Shi J [11]
  • Bocking T [10]
  • Chaban Y [10]
  • Monnie C [10]
  • Nesterova T [10]
  • Ni T [10]
  • Parker MW [10]
  • Shen J [10]
  • Yang Z [10]
  • Devarkar SC [9]
  • Hardenbrook N [9]
  • Kleinpeter AB [9]
  • Lucic A [9]
  • Meshkin H [9]
  • Meuser ME [9]
  • Schulten K [9]
  • Xu J [9]
  • Yang R [9]
  • Hope J [8]
  • Parker WM [8]
  • Perilla RJ [8]
  • Dick RA [7]
  • Ricana CL [7]
  • Briggs JAG [6]
  • Broad AM [6]
  • Engelman AN [6]
  • Feathers JR [6]
  • Freed OE [6]
  • Gronenborn AM [6]
  • Johnson MC [6]
  • Kravchuk V [6]
  • Lyddon TD [6]
  • Morado DR [6]
  • Schur FKM [6]
  • Vogt VM [6]
  • Akil C [5]
  • Arizaga F [5]
  • Arizaga Jr F [5]
  • Chenavier F [5]
  • Cherepanov P [5]
  • Cook M [5]
  • Cook NJ [5]
  • Hikichi Y [5]
  • Hou Z [5]
  • Li Z [5]
  • Masino L [5]
  • Maslen S [5]
  • Nans A [5]
  • Punch E [5]
  • Singer MR [5]
  • Skehel M [5]
  • Smith J [5]
  • Taylor IA [5]
  • Veler H [5]
  • Zanetti G [5]
  • Zhao G [5]
  • Zhou Z [5]
  • Chen B [4]
  • Himes BA [4]
  • Hou G [4]
  • Polenova T [4]
  • Alvarez FJ [3]
  • Cassidy CK [3]
  • Harding EF [3]
  • Katzourakis A [3]
  • Lu M [3]
  • Lyu C [3]
  • Ma J [3]
  • Peeples CA [3]
  • Ramezani A [3]
  • Zhang Z [3]
  • Zhou G [3]
  • Arndt WG [2]
  • Bedwell GJ [2]
  • Dumoux M [2]
  • Elad N [2]
  • Liu C [2]
  • Mansky LM [2]
  • Meng X [2]
  • Prevelige Jr Pe [2]
  • Ramalhu R [2]
  • Rousso I [2]
  • Talledge N [2]
  • Yang H [2]
  • Yu G [2]
  • Yufenyuy E [2]

Author by ORCID

  • Perilla JR [53]
  • Zhang P [33]
  • Rey JS [29]
  • Zhu Y [19]
  • Xu C [16]
  • Xiong Y [14]
  • Wu C [14]
  • Freniere C [13]
  • Chen L [10]
  • Yang Z [10]
  • Ni T [10]
  • Monnie C [10]
  • Shen Y [10]
  • Nesterova T [10]
  • Parker MW [10]
  • Bocking T [10]
  • Freed EO [10]
  • Ahn J [10]
  • Kleinpeter AB [9]
  • Xu J [9]
  • Hardenbrook N [9]
  • Ricana CL [7]
  • Dick RA [7]
  • Broad AM [6]
  • Kravchuk V [6]
  • Feathers JR [6]
  • Johnson MC [6]
  • Briggs JAG [6]
  • Morado DR [6]
  • Schur FKM [6]
  • Cherepanov P [5]
  • Cook NJ [5]
  • Nans A [5]
  • Masino L [5]
  • Taylor IA [5]
  • Chenavier F [5]
  • Engelman AN [5]
  • Zanetti G [5]
  • Hope J [5]
  • Zhou Z [5]
  • Himes BA [4]
  • Gronenborn AM [4]
  • Cassidy CK [3]
  • Alvarez FJ [3]
  • Ramezani A [3]
  • Chen B [2]
  • Arndt WG [2]
  • Polenova T [2]
  • Ramalhu R [2]
  • Zhang W [2]
  • Yang H [2]
  • Mansky LM [2]
  • Ekbataniamiri F [1]
  • Elad N [1]
  • Hou Z [1]
  • Bedwell GJ [1]
  • Hou G [1]
  • Faerch M [1]
  • Rousso I [1]
  • Alvarez FJD [1]
  • Wang M [1]
  • Meuser ME [1]
  • Dumoux M [1]
  • Hikichi Y [1]
  • Brancato SG [1]
  • Akil C [1]
  • Jang S [1]
  • Highland CM [1]
  • Torbett BE [1]
  • Ambrus K [1]
  • Veler H [1]

Journal

  • BIORXIV [19]
  • NAT COMMUN [16]
  • J AM CHEM SOC [13]
  • SCI ADV [12]
  • NATURE [7]
  • PLOS PATHOG [6]
  • ELIFE [3]
  • TO BE PUBLISHED [3]
  • J PHYS CHEM B [1]

Software

  • CRYOSPARC [16]
  • RELION [8]
  • CTFFIND [7]
  • IMOD [5]
  • AV3 [4]
  • MATLAB [4]
  • TOM TOOLBOX [4]
  • NOVACTF [3]
  • CHIMERA [2]
  • CTFPHASEFLIP [2]
  • EMAN [2]
  • FREALIGN [2]
  • SPIDER, IHRSR [2]
  • UCSF CHIMERAX [2]
  • DYNAMO [1]
  • EMCLARITY [1]
  • MD [1]
  • MDFF [1]
  • PYTOM [1]
  • TOMO3D [1]
  • WARP [1]

Microscope

  • TFS KRIOS [32]
  • FEI TITAN KRIOS [23]
  • FEI POLARA 300 [7]
  • TFS GLACIOS [3]
  • FEI TECNAI F20 [2]

Electron Source

  • FIELD EMISSION GUN [67]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [21]
  • FEI FALCON IV 4K X 4K [16]
  • GATAN K2 QUANTUM 4K X 4K [14]
  • GATAN ULTRASCAN 4000 4K X 4K [4]
  • KODAK SO-163 FILM [4]
  • GATAN K3 6K X 4K [3]
  • GATAN K2 SUMMIT 4K X 4K [2]
  • FEI FALCON II 4K X 4K [1]
  • GATAN K3 BIOCONTINUUM 6K X 4K [1]
  • TFS FALCON 4I 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [1]

EMPIAR Image category

  • TILT SERIES [1]

External links

  • PDB [64]
  • UniProt [31]
  • PDBe-Kb [30]
  • InterPro [23]
  • ChEBI [12]
  • ChEMBL [12]
  • DrugBank [12]
  • Gene Ontology [8]
  • Pfam [8]
  • AlphaFold DB [5]
  • EMPIAR [3]
  • EMDB [1]
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EMD-59277
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3D View
Cryo-ET STA of mature HERV-K hexameric capsomer
CryoEM
Release date: Aug. 26, 2026
Resolution: 6.2 Å
EM Method: Subtomogram averaging

Lyu C, Peeples CA, Zhang Z, Shen Y, Hou Z, Harding EF, Hope J, Perilla JR, Katzourakis A, Zhang P

To Be Published

EMD-59279
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3D View
Cryo-EM structure of native, mature HERV-K pentameric capsomer
CryoEM
Release date: Aug. 19, 2026
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 32yy
Q-score: 0.436
Similar entry percentile: 71%

Lyu C, Peeples CA, Zhang Z, Shen Y, Hou Z, Harding EF, Hope J, Perilla JR, Katzourakis A, Zhang P

To Be Published

EMD-59280
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3D View
Cryo-EM structure of native, mature HERV-K hexameric capsomer
CryoEM
Release date: Aug. 19, 2026
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 32zb
Q-score: 0.4
Similar entry percentile: 22%

Lyu C, Peeples CA, Zhang Z, Shen Y, Hou Z, Harding EF, Hope J, Perilla JR, Katzourakis A, Zhang P

To Be Published

EMD-71417
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3D View
Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles
CryoEM
Release date: April 29, 2026
Resolution: 2.28 Å
EM Method: Single-particle
Fitted PDBs: 9p9l
Q-score: 0.587
Similar entry percentile: 50%

Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y

J Am Chem Soc (2025) 147 pp. 42685-42700 [ Pubmed: 41198571 DOI: doi:10.1021/jacs.5c13735 ]

EMD-71418
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CA-SP1 immature lattice assembled in vitro with inhibitor lenacapavir dialyzed to 50nM
CryoEM
Release date: April 29, 2026
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 9p9m
Q-score: 0.51
Similar entry percentile: 55%

Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y

J Am Chem Soc (2025) 147 pp. 42685-42700 [ Pubmed: 41198571 DOI: doi:10.1021/jacs.5c13735 ]

EMD-48430
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SPA of purified HIV-1 CA protein in vitro assembled with IP6 mature morphology . 500 uM LEN was added post assembly.
CryoEM
Release date: Jan. 14, 2026
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9mnm
Q-score: 0.148
Similar entry percentile: 1%

Ricana CL, Brancato SG, Highland CM, Ekbataniamiri F, Ambrus K, Rey JS, Faerch M, Torbett BE, Perilla JR, Dick RA

bioRxiv (2026) [ DOI: doi:10.64898/2026.03.02.709178 Pubmed: 41867786 ]

EMD-48795
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Subtomogram averaging of HTLV-1 Gag capsid from immature particles
CryoEM
Release date: Dec. 24, 2025
Resolution: 7.82 Å
EM Method: Subtomogram averaging

Arndt WG, Ramezani A, Talledge N, Yu G, Yang H, Chen B, Perilla JR, Zhang W, Mansky LM

Nat Commun (2025) 17 pp. 444-444 [ DOI: doi:10.1038/s41467-025-67129-1 Pubmed: 41381513 ]

EMD-48796
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HTLV-1 Gag capsid from immature particles
CryoEM
Release date: Dec. 24, 2025
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 9n0w
Q-score: 0.367
Similar entry percentile: 20%

Arndt WG, Ramezani A, Talledge N, Yu G, Yang H, Chen B, Perilla JR, Zhang W, Mansky LM

Nat Commun (2025) 17 pp. 444-444 [ DOI: doi:10.1038/s41467-025-67129-1 Pubmed: 41381513 ]

EMD-54067
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SIVtal integrase in complex with RNA stem-loop double filament reconstructed by global refinement
CryoEM
Release date: Dec. 10, 2025
Resolution: 3.74 Å
EM Method: Single-particle

Singer MR, Li Z, Rey JS, Hope J, Chenavier F, Cook NJ, Punch E, Smith J, Zhou Z, Maslen S, Masino L, Nans A, Skehel M, Taylor IA, Zanetti G, Zhang P, Perilla JR, Engelman AN, Cherepanov P

Nature (2026) 652 pp. 1068-1075 [ DOI: doi:10.1038/s41586-026-10154-x Pubmed: 41708858 ]

EMD-54068
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SIVtal integrase in complex with RNA stem-loop focused refinement of the filament repeat unit
CryoEM
Release date: Dec. 10, 2025
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9rmu
Q-score: 0.546
Similar entry percentile: 88%

Singer MR, Li Z, Rey JS, Hope J, Chenavier F, Cook NJ, Punch E, Smith J, Zhou Z, Maslen S, Masino L, Nans A, Skehel M, Taylor IA, Zanetti G, Zhang P, Perilla JR, Engelman AN, Cherepanov P

Nature (2026) 652 pp. 1068-1075 [ DOI: doi:10.1038/s41586-026-10154-x Pubmed: 41708858 ]

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Filter By

Current Database

  • EMDB [67]
  • EMPIAR [1]

Current status

  • REL [68]

Sample type

  • Virus [51]
  • Protein [48]
  • Ligand [14]
  • Complex [10]
  • Sample [7]
  • RNA [1]

Organism

  • Human immunodeficiency virus 1 [22]
  • Human immunodeficiency virus 1 [10]
  • Human immunodeficiency virus 1 [9]
  • Equine infectious anemia virus [6]
  • Human endogenous retrovirus k [4]
  • Human immunodeficiency virus 1 [3]
  • Escherichia coli [3]
  • Caprine arthritis encephalitis virus [2]
  • Simian immunodeficiency virus [2]
  • Primate t-lymphotropic virus 1 [2]
  • Visna-maedi virus [2]
  • Uncultured virus [2]
  • Equine infectious anemia virus [1]
  • Human immunodeficiency virus 1 [1]
  • Chlamydomonas reinhardtii [1]
  • Synthetic construct [1]
  • Homo sapiens [1]

EM Method

  • Subtomogram averaging [32]
  • Single-particle [25]
  • Helical reconstruction [6]
  • Tomography [4]

Resolution

  • ≥ 2Å and < 3Å [8]
  • ≥ 3Å and < 4Å [23]
  • ≥ 4Å and < 5Å [7]
  • ≥ 5Å and < 6Å [4]
  • ≥ 6Å and < 8Å [6]
  • ≥ 8Å and < 12Å [13]
  • ≥ 12Å and < 16Å [1]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 50-100 kDa [1]
  • 100-250 kDa [6]
  • 250-500 kDa [13]
  • 500-1000 kDa [6]
  • 1-2 MDa [1]
  • 2-5 MDa [1]
  • 5-10 MDa [1]
  • > 10 MDa [1]

Release Date

  • 2026 [6]
  • 2025 [28]
  • 2024 [7]
  • 2023 [1]
  • 2021 [10]
  • 2020 [6]
  • 2018 [1]
  • 2017 [2]
  • 2016 [2]
  • 2015 [3]
  • 2013 [2]

Author by name

  • Perilla JR [67]
  • Zhang P [44]
  • Rey JS [35]
  • Zhu Y [24]
  • Shen Y [17]
  • Xu C [16]
  • Freed EO [15]
  • Ning J [15]
  • Ahn J [14]
  • Aiken C [14]
  • Chen L [14]
  • Freniere C [14]
  • Wu C [14]
  • Xiong Y [14]
  • Shi J [11]
  • Bocking T [10]
  • Chaban Y [10]
  • Monnie C [10]
  • Nesterova T [10]
  • Ni T [10]
  • Parker MW [10]
  • Shen J [10]
  • Yang Z [10]
  • Devarkar SC [9]
  • Hardenbrook N [9]
  • Kleinpeter AB [9]
  • Lucic A [9]
  • Meshkin H [9]
  • Meuser ME [9]
  • Schulten K [9]
  • Xu J [9]
  • Yang R [9]
  • Hope J [8]
  • Parker WM [8]
  • Perilla RJ [8]
  • Dick RA [7]
  • Ricana CL [7]
  • Briggs JAG [6]
  • Broad AM [6]
  • Engelman AN [6]
  • Feathers JR [6]
  • Freed OE [6]
  • Gronenborn AM [6]
  • Johnson MC [6]
  • Kravchuk V [6]
  • Lyddon TD [6]
  • Morado DR [6]
  • Schur FKM [6]
  • Vogt VM [6]
  • Akil C [5]
  • Arizaga F [5]
  • Arizaga Jr F [5]
  • Chenavier F [5]
  • Cherepanov P [5]
  • Cook M [5]
  • Cook NJ [5]
  • Hikichi Y [5]
  • Hou Z [5]
  • Li Z [5]
  • Masino L [5]
  • Maslen S [5]
  • Nans A [5]
  • Punch E [5]
  • Singer MR [5]
  • Skehel M [5]
  • Smith J [5]
  • Taylor IA [5]
  • Veler H [5]
  • Zanetti G [5]
  • Zhao G [5]
  • Zhou Z [5]
  • Chen B [4]
  • Himes BA [4]
  • Hou G [4]
  • Polenova T [4]
  • Alvarez FJ [3]
  • Cassidy CK [3]
  • Harding EF [3]
  • Katzourakis A [3]
  • Lu M [3]
  • Lyu C [3]
  • Ma J [3]
  • Peeples CA [3]
  • Ramezani A [3]
  • Zhang Z [3]
  • Zhou G [3]
  • Arndt WG [2]
  • Bedwell GJ [2]
  • Dumoux M [2]
  • Elad N [2]
  • Liu C [2]
  • Mansky LM [2]
  • Meng X [2]
  • Prevelige Jr Pe [2]
  • Ramalhu R [2]
  • Rousso I [2]
  • Talledge N [2]
  • Yang H [2]
  • Yu G [2]
  • Yufenyuy E [2]

Author by ORCID

  • Perilla JR [53]
  • Zhang P [33]
  • Rey JS [29]
  • Zhu Y [19]
  • Xu C [16]
  • Xiong Y [14]
  • Wu C [14]
  • Freniere C [13]
  • Chen L [10]
  • Yang Z [10]
  • Ni T [10]
  • Monnie C [10]
  • Shen Y [10]
  • Nesterova T [10]
  • Parker MW [10]
  • Bocking T [10]
  • Freed EO [10]
  • Ahn J [10]
  • Kleinpeter AB [9]
  • Xu J [9]
  • Hardenbrook N [9]
  • Ricana CL [7]
  • Dick RA [7]
  • Broad AM [6]
  • Kravchuk V [6]
  • Feathers JR [6]
  • Johnson MC [6]
  • Briggs JAG [6]
  • Morado DR [6]
  • Schur FKM [6]
  • Cherepanov P [5]
  • Cook NJ [5]
  • Nans A [5]
  • Masino L [5]
  • Taylor IA [5]
  • Chenavier F [5]
  • Engelman AN [5]
  • Zanetti G [5]
  • Hope J [5]
  • Zhou Z [5]
  • Himes BA [4]
  • Gronenborn AM [4]
  • Cassidy CK [3]
  • Alvarez FJ [3]
  • Ramezani A [3]
  • Chen B [2]
  • Arndt WG [2]
  • Polenova T [2]
  • Ramalhu R [2]
  • Zhang W [2]
  • Yang H [2]
  • Mansky LM [2]
  • Ekbataniamiri F [1]
  • Elad N [1]
  • Hou Z [1]
  • Bedwell GJ [1]
  • Hou G [1]
  • Faerch M [1]
  • Rousso I [1]
  • Alvarez FJD [1]
  • Wang M [1]
  • Meuser ME [1]
  • Dumoux M [1]
  • Hikichi Y [1]
  • Brancato SG [1]
  • Akil C [1]
  • Jang S [1]
  • Highland CM [1]
  • Torbett BE [1]
  • Ambrus K [1]
  • Veler H [1]

Journal

  • BIORXIV [19]
  • NAT COMMUN [16]
  • J AM CHEM SOC [13]
  • SCI ADV [12]
  • NATURE [7]
  • PLOS PATHOG [6]
  • ELIFE [3]
  • TO BE PUBLISHED [3]
  • J PHYS CHEM B [1]

Software

  • CRYOSPARC [16]
  • RELION [8]
  • CTFFIND [7]
  • IMOD [5]
  • AV3 [4]
  • MATLAB [4]
  • TOM TOOLBOX [4]
  • NOVACTF [3]
  • CHIMERA [2]
  • CTFPHASEFLIP [2]
  • EMAN [2]
  • FREALIGN [2]
  • SPIDER, IHRSR [2]
  • UCSF CHIMERAX [2]
  • DYNAMO [1]
  • EMCLARITY [1]
  • MD [1]
  • MDFF [1]
  • PYTOM [1]
  • TOMO3D [1]
  • WARP [1]

Microscope

  • TFS KRIOS [32]
  • FEI TITAN KRIOS [23]
  • FEI POLARA 300 [7]
  • TFS GLACIOS [3]
  • FEI TECNAI F20 [2]

Electron Source

  • FIELD EMISSION GUN [67]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [21]
  • FEI FALCON IV 4K X 4K [16]
  • GATAN K2 QUANTUM 4K X 4K [14]
  • GATAN ULTRASCAN 4000 4K X 4K [4]
  • KODAK SO-163 FILM [4]
  • GATAN K3 6K X 4K [3]
  • GATAN K2 SUMMIT 4K X 4K [2]
  • FEI FALCON II 4K X 4K [1]
  • GATAN K3 BIOCONTINUUM 6K X 4K [1]
  • TFS FALCON 4I 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [1]

EMPIAR Image category

  • TILT SERIES [1]

External links

  • PDB [64]
  • UniProt [31]
  • PDBe-Kb [30]
  • InterPro [23]
  • ChEBI [12]
  • ChEMBL [12]
  • DrugBank [12]
  • Gene Ontology [8]
  • Pfam [8]
  • AlphaFold DB [5]
  • EMPIAR [3]
  • EMDB [1]