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natural_source_ncbi_code:"1496"

Filter By

Current Database

  • EMDB [67]

Current status

  • REL [67]

Sample type

  • Complex [62]
  • Protein [57]
  • Ligand [18]
  • Cellular component [11]
  • Other [5]

Organism

  • Clostridioides difficile [67]
  • Homo sapiens [8]
  • Synthetic construct [5]
  • Clostridioides difficile [3]
  • Priestia megaterium [2]
  • Mus musculus [1]
  • Clostridioides phage phicd508 [1]
  • Escherichia coli [1]
  • Spodoptera frugiperda [1]
  • Drosophila melanogaster [1]

EM Method

  • Single-particle [65]
  • Helical reconstruction [2]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [35]
  • ≥ 4Å and < 5Å [10]
  • ≥ 5Å and < 6Å [4]
  • ≥ 6Å and < 8Å [2]
  • ≥ 8Å and < 12Å [1]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 100-250 kDa [1]
  • 250-500 kDa [17]
  • 500-1000 kDa [17]
  • 1-2 MDa [19]
  • > 10 MDa [2]

Release Date

  • 2025 [16]
  • 2024 [20]
  • 2023 [3]
  • 2022 [14]
  • 2021 [2]
  • 2020 [3]
  • 2019 [7]
  • 2018 [2]

Author by name

  • Bullough PA [12]
  • Fagan RP [12]
  • Fortier LC [12]
  • Wilson JS [12]
  • Cai X [10]
  • Cai XY [10]
  • He Y [10]
  • Imani A [10]
  • Miller JF [10]
  • Scholl D [10]
  • Yu I [10]
  • Zhang J [10]
  • Zhou ZH [10]
  • Jiang M [9]
  • Lacy DB [9]
  • Sheedlo MJ [9]
  • Anderson DM [8]
  • Dong M [8]
  • Jensen JL [8]
  • Bous J [7]
  • Gratz L [7]
  • Kinsolving J [7]
  • Kosenina S [7]
  • Kozielewicz P [7]
  • Masuyer G [7]
  • Schulte G [7]
  • Shekhani R [7]
  • Stenmark P [7]
  • Wang Y [7]
  • Adipietro KA [5]
  • Kato T [5]
  • Kawamoto A [5]
  • Pozharski E [5]
  • Rustandi RR [5]
  • Sato Y [5]
  • Tao L [5]
  • Tsuge H [5]
  • Varney KM [5]
  • Weber DJ [5]
  • Yamada T [5]
  • Yoshida T [5]
  • Zhang Y [5]
  • Luo J [4]
  • Yang Q [4]
  • Abeyawardhane DL [3]
  • Baker D [3]
  • Borst AJ [3]
  • Carr KD [3]
  • Melnyk RA [3]
  • Ragotte RJ [3]
  • Ruiz RG [3]
  • Silin VI [3]
  • Tam J [3]
  • Weidle C [3]
  • Beckett D [2]
  • Beilhartz GL [2]
  • Ben-hail D [2]
  • Berman JM [2]
  • Christanti S [2]
  • Cleveland T [2]
  • Cook ME [2]
  • Coventry B [2]
  • Georges AD [2]
  • Glogl M [2]
  • Godoy-ruiz R [2]
  • Grishaev A [2]
  • He L [2]
  • Huang J [2]
  • Jin D [2]
  • Kristopeit A [2]
  • Lancaster C [2]
  • Li D [2]
  • Li Y [2]
  • Li Z [2]
  • Liang H [2]
  • Loughney JW [2]
  • Lu P [2]
  • Lu PL [2]
  • Lv X [2]
  • Lv XC [2]
  • Mackerell AD [2]
  • Michel SLJ [2]
  • Miletic S [2]
  • Neu HM [2]
  • Olson JW [2]
  • Palou R [2]
  • Peralta C [2]
  • Roth BM [2]
  • Rubinstein JL [2]
  • Schramek D [2]
  • Sun K [2]
  • Tyers M [2]
  • Wan L [2]
  • Wang X [2]
  • Wilder PT [2]
  • Xu X [2]
  • Yu W [2]
  • Zhan X [2]
  • Zhang X [2]
  • Zhen Y [2]

Author by ORCID

  • Bullough PA [12]
  • Wilson JS [12]
  • Fagan RP [12]
  • Fortier LC [12]
  • Cai X [10]
  • He Y [10]
  • Zhou ZH [10]
  • Miller JF [10]
  • Lacy DB [8]
  • Gratz L [7]
  • Kinsolving J [7]
  • Schulte G [7]
  • Bous J [7]
  • Jensen JL [7]
  • Masuyer G [7]
  • Yoshida T [5]
  • Yamada T [5]
  • Kawamoto A [5]
  • Kato T [5]
  • Tsuge H [5]
  • Tao L [5]
  • Lv X [2]
  • Lu P [2]
  • Berman JM [2]
  • Yu W [2]
  • Glogl M [2]
  • Liang H [2]
  • Palou R [2]
  • Baker D [2]
  • Cook ME [2]
  • Michel SLJ [2]
  • Ragotte RJ [2]
  • Melnyk RA [2]
  • Zhang Y [2]
  • Beilhartz GL [2]
  • Ben-hail D [2]
  • Weber DJ [2]
  • Xu X [2]
  • He L [2]
  • Rubinstein JL [2]
  • Cleveland T [2]
  • Zhan X [2]
  • Luo J [2]
  • Borst AJ [2]
  • Godoy-ruiz R [2]
  • Peralta C [2]
  • Carr KD [2]
  • Tian S [1]
  • Zeng J [1]
  • Chen Z [1]
  • Yu H [1]
  • Dong M [1]
  • Huang L [1]
  • Gribenko A [1]
  • Boesen T [1]
  • Chen P [1]
  • Zhang Y [1]
  • Jin R [1]
  • Jorgensen R [1]

Journal

  • NAT COMMUN [18]
  • LIFE SCI ALLIANCE [12]
  • TO BE PUBLISHED [12]
  • CELL REP [7]
  • NAT MICROBIOL [7]
  • PNAS [5]
  • CELL [2]
  • EMBO REP [1]
  • INFECT.IMMUN. [1]
  • NATURE [1]
  • PLOS BIOL [1]

Software

  • CRYOSPARC [18]
  • RELION [10]
  • CTFFIND [1]
  • GCTF [1]

Microscope

  • FEI TITAN KRIOS [47]
  • TFS KRIOS [14]
  • TFS GLACIOS [4]
  • FEI TECNAI F20 [2]
  • JEOL 3200FSC [1]

Electron Source

  • FIELD EMISSION GUN [67]

Film or detector model

  • GATAN K3 6K X 4K [49]
  • GATAN K2 SUMMIT 4K X 4K [15]
  • GATAN K3 BIOQUANTUM 6K X 4K [2]
  • FEI FALCON IV 4K X 4K [1]

External links

  • PDB [56]
  • UniProt [56]
  • PDBe-Kb [55]
  • AlphaFold DB [54]
  • Pfam [50]
  • InterPro [48]
  • Gene Ontology [30]
  • ChEBI [18]
  • DrugBank [18]
  • ChEMBL [6]
  • EMPIAR [4]
Sort by: Download
Showing 1 - 10 of 67. Page 1 of 7
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EMD-49373
Download Map
3D View
CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B TcdB
Release date: Nov. 12, 2025
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9nfu
Q-score: 0.453

Bennett NR, Watson JL, Ragotte RJ, Borst AJ, See DL, Weidle C, Biswas R, Yu Y, Shrock EL, Ault R, Leung PJY, Huang B, Goreshnik I, Tam J, Carr KD, Singer B, Criswell C, Wicky BIM, Vafeados D, Garcia Sanchez M, Kim HM, Vazquez Torres S, Chan S, Sun SM, Spear TT, Sun Y, O'Reilly K, Maris JM, Sgourakis NG, Melnyk RA, Liu CC, Baker D

Nature (2026) 649 pp. 183-193 [ Pubmed: 41193805 DOI: doi:10.1038/s41586-025-09721-5 ]

EMD-48223
Download Map
3D View
De novo designed minibinder complexed with Clostridioides difficile Toxin B
Release date: Sept. 17, 2025
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 9mf4
Q-score: 0.49

Ragotte RJ, Liang H, Tam J, Miletic S, Berman JM, Palou R, Weidle C, Li Z, Glogl M, Beilhartz GL, Carr KD, Borst AJ, Coventry B, Wang X, Rubinstein JL, Tyers M, Schramek D, Melnyk RA, Baker D

PNAS (2025) 122 pp. e2509329122-e2509329122 [ DOI: doi:10.1073/pnas.2509329122 Pubmed: 40982695 ]

EMD-48707
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3D View
Clostridioides difficile Toxin A with mCDIFA-248-25 Fab
Release date: July 9, 2025
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9mx1
Q-score: 0.45

Kroh HK, Jensen JL, Wellnitz S, Park JJ, Esadze A, Huynh KW, Ammirati M, Han S, Anderson AS, Lacy DB, Gribenko A

Infect.Immun. (2025) 93 pp. e0013925-e0013925 [ DOI: doi:10.1128/iai.00139-25 Pubmed: 40844461 ]

EMD-45739
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3D View
CryoEM Strucuture of TcdB in complex with De Novo Minibinder fzd48
Release date: May 21, 2025
Resolution: 4.61 Å
EM Method: Single-particle
Fitted PDBs: 9cm5
Q-score: 0.235

Ragotte RJ, Liang H, Tam J, Miletic S, Berman JM, Palou R, Weidle C, Li Z, Glogl M, Beilhartz GL, Carr KD, Borst AJ, Coventry B, Wang X, Rubinstein JL, Tyers M, Schramek D, Melnyk RA, Baker D

PNAS (2025) 122 pp. e2509329122-e2509329122 [ DOI: doi:10.1073/pnas.2509329122 Pubmed: 40982695 ]

EMD-51138
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3D View
C3 reconstruction of extended phiCD508 needle
Release date: April 9, 2025
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 9g8s
Q-score: 0.397

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

EMD-51201
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3D View
Contracted phiCD508 tail
Release date: April 9, 2025
Resolution: 4.11 Å
EM Method: Single-particle
Fitted PDBs: 9gb8
Q-score: 0.246

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

EMD-51191
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3D View
Extended phiCD508 capsid
Release date: March 26, 2025
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 9gay
Q-score: 0.203

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

EMD-51192
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3D View
Contracted phiCD508 capsid
Release date: March 26, 2025
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 9gaz
Q-score: 0.528

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

EMD-51193
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3D View
Extended phiCD508 portal adjacent capsid
Release date: March 26, 2025
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 9gb0
Q-score: 0.509

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

EMD-51194
Download Map
3D View
Extended phiCD508 tail
Release date: March 26, 2025
Resolution: 2.71 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gb1
Q-score: 0.38

Wilson JS, Fortier LC, Fagan RP, Bullough PA

Life Sci Alliance (2025) 8 [ Pubmed: 40139691 DOI: doi:10.26508/lsa.202403088 ]

Sort by: Download
Showing 1 - 10 of 67. Page 1 of 7
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [67]

Current status

  • REL [67]

Sample type

  • Complex [62]
  • Protein [57]
  • Ligand [18]
  • Cellular component [11]
  • Other [5]

Organism

  • Clostridioides difficile [67]
  • Homo sapiens [8]
  • Synthetic construct [5]
  • Clostridioides difficile [3]
  • Priestia megaterium [2]
  • Mus musculus [1]
  • Clostridioides phage phicd508 [1]
  • Escherichia coli [1]
  • Spodoptera frugiperda [1]
  • Drosophila melanogaster [1]

EM Method

  • Single-particle [65]
  • Helical reconstruction [2]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [35]
  • ≥ 4Å and < 5Å [10]
  • ≥ 5Å and < 6Å [4]
  • ≥ 6Å and < 8Å [2]
  • ≥ 8Å and < 12Å [1]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 100-250 kDa [1]
  • 250-500 kDa [17]
  • 500-1000 kDa [17]
  • 1-2 MDa [19]
  • > 10 MDa [2]

Release Date

  • 2025 [16]
  • 2024 [20]
  • 2023 [3]
  • 2022 [14]
  • 2021 [2]
  • 2020 [3]
  • 2019 [7]
  • 2018 [2]

Author by name

  • Bullough PA [12]
  • Fagan RP [12]
  • Fortier LC [12]
  • Wilson JS [12]
  • Cai X [10]
  • Cai XY [10]
  • He Y [10]
  • Imani A [10]
  • Miller JF [10]
  • Scholl D [10]
  • Yu I [10]
  • Zhang J [10]
  • Zhou ZH [10]
  • Jiang M [9]
  • Lacy DB [9]
  • Sheedlo MJ [9]
  • Anderson DM [8]
  • Dong M [8]
  • Jensen JL [8]
  • Bous J [7]
  • Gratz L [7]
  • Kinsolving J [7]
  • Kosenina S [7]
  • Kozielewicz P [7]
  • Masuyer G [7]
  • Schulte G [7]
  • Shekhani R [7]
  • Stenmark P [7]
  • Wang Y [7]
  • Adipietro KA [5]
  • Kato T [5]
  • Kawamoto A [5]
  • Pozharski E [5]
  • Rustandi RR [5]
  • Sato Y [5]
  • Tao L [5]
  • Tsuge H [5]
  • Varney KM [5]
  • Weber DJ [5]
  • Yamada T [5]
  • Yoshida T [5]
  • Zhang Y [5]
  • Luo J [4]
  • Yang Q [4]
  • Abeyawardhane DL [3]
  • Baker D [3]
  • Borst AJ [3]
  • Carr KD [3]
  • Melnyk RA [3]
  • Ragotte RJ [3]
  • Ruiz RG [3]
  • Silin VI [3]
  • Tam J [3]
  • Weidle C [3]
  • Beckett D [2]
  • Beilhartz GL [2]
  • Ben-hail D [2]
  • Berman JM [2]
  • Christanti S [2]
  • Cleveland T [2]
  • Cook ME [2]
  • Coventry B [2]
  • Georges AD [2]
  • Glogl M [2]
  • Godoy-ruiz R [2]
  • Grishaev A [2]
  • He L [2]
  • Huang J [2]
  • Jin D [2]
  • Kristopeit A [2]
  • Lancaster C [2]
  • Li D [2]
  • Li Y [2]
  • Li Z [2]
  • Liang H [2]
  • Loughney JW [2]
  • Lu P [2]
  • Lu PL [2]
  • Lv X [2]
  • Lv XC [2]
  • Mackerell AD [2]
  • Michel SLJ [2]
  • Miletic S [2]
  • Neu HM [2]
  • Olson JW [2]
  • Palou R [2]
  • Peralta C [2]
  • Roth BM [2]
  • Rubinstein JL [2]
  • Schramek D [2]
  • Sun K [2]
  • Tyers M [2]
  • Wan L [2]
  • Wang X [2]
  • Wilder PT [2]
  • Xu X [2]
  • Yu W [2]
  • Zhan X [2]
  • Zhang X [2]
  • Zhen Y [2]

Author by ORCID

  • Bullough PA [12]
  • Wilson JS [12]
  • Fagan RP [12]
  • Fortier LC [12]
  • Cai X [10]
  • He Y [10]
  • Zhou ZH [10]
  • Miller JF [10]
  • Lacy DB [8]
  • Gratz L [7]
  • Kinsolving J [7]
  • Schulte G [7]
  • Bous J [7]
  • Jensen JL [7]
  • Masuyer G [7]
  • Yoshida T [5]
  • Yamada T [5]
  • Kawamoto A [5]
  • Kato T [5]
  • Tsuge H [5]
  • Tao L [5]
  • Lv X [2]
  • Lu P [2]
  • Berman JM [2]
  • Yu W [2]
  • Glogl M [2]
  • Liang H [2]
  • Palou R [2]
  • Baker D [2]
  • Cook ME [2]
  • Michel SLJ [2]
  • Ragotte RJ [2]
  • Melnyk RA [2]
  • Zhang Y [2]
  • Beilhartz GL [2]
  • Ben-hail D [2]
  • Weber DJ [2]
  • Xu X [2]
  • He L [2]
  • Rubinstein JL [2]
  • Cleveland T [2]
  • Zhan X [2]
  • Luo J [2]
  • Borst AJ [2]
  • Godoy-ruiz R [2]
  • Peralta C [2]
  • Carr KD [2]
  • Tian S [1]
  • Zeng J [1]
  • Chen Z [1]
  • Yu H [1]
  • Dong M [1]
  • Huang L [1]
  • Gribenko A [1]
  • Boesen T [1]
  • Chen P [1]
  • Zhang Y [1]
  • Jin R [1]
  • Jorgensen R [1]

Journal

  • NAT COMMUN [18]
  • LIFE SCI ALLIANCE [12]
  • TO BE PUBLISHED [12]
  • CELL REP [7]
  • NAT MICROBIOL [7]
  • PNAS [5]
  • CELL [2]
  • EMBO REP [1]
  • INFECT.IMMUN. [1]
  • NATURE [1]
  • PLOS BIOL [1]

Software

  • CRYOSPARC [18]
  • RELION [10]
  • CTFFIND [1]
  • GCTF [1]

Microscope

  • FEI TITAN KRIOS [47]
  • TFS KRIOS [14]
  • TFS GLACIOS [4]
  • FEI TECNAI F20 [2]
  • JEOL 3200FSC [1]

Electron Source

  • FIELD EMISSION GUN [67]

Film or detector model

  • GATAN K3 6K X 4K [49]
  • GATAN K2 SUMMIT 4K X 4K [15]
  • GATAN K3 BIOQUANTUM 6K X 4K [2]
  • FEI FALCON IV 4K X 4K [1]

External links

  • PDB [56]
  • UniProt [56]
  • PDBe-Kb [55]
  • AlphaFold DB [54]
  • Pfam [50]
  • InterPro [48]
  • Gene Ontology [30]
  • ChEBI [18]
  • DrugBank [18]
  • ChEMBL [6]
  • EMPIAR [4]