9NDY | pdb_00009ndy

Composite baseplate asymmetric unit of JohannRWettstein (Bas63)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Icosahedral capsid assembly of phage JohannRWettstein (Bas63)

Hodgkinson-Bean, J., Ayala, R., McJarrow-Keller, K., Cassin, L., Rutter, G.L., Crowe, A.J.M., Wolf, M., Bostina, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 597.97 kDa 
  • Atom Count: 30,166 
  • Modeled Residue Count: 4,160 
  • Deposited Residue Count: 5,434 
  • Unique protein chains: 9

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tube initiator protein (gp018)
A, B
265Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE7VVH7 (Escherichia phage JohannRWettstein)
Explore A0AAE7VVH7 
Go to UniProtKB:  A0AAE7VVH7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE7VVH7
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sheath initiator (gp022)
C, D
139Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE8B0J9 (Escherichia phage JohannRWettstein)
Explore A0AAE8B0J9 
Go to UniProtKB:  A0AAE8B0J9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE8B0J9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Hub protein (gp020)325Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE7VWE1 (Escherichia phage JohannRWettstein)
Explore A0AAE7VWE1 
Go to UniProtKB:  A0AAE7VWE1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE7VWE1
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tape measure protein (gp017)742Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE7VV46 (Escherichia phage JohannRWettstein)
Explore A0AAE7VV46 
Go to UniProtKB:  A0AAE7VV46
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE7VV46
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Puncture apparatus (gp021)207Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE8B143 (Escherichia phage JohannRWettstein)
Explore A0AAE8B143 
Go to UniProtKB:  A0AAE8B143
Entity Groups
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UniProt GroupA0AAE8B143
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Wedge protein 2 (gp023)
H, I, K, L
489Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE8B2A9 (Escherichia phage JohannRWettstein)
Explore A0AAE8B2A9 
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UniProt GroupA0AAE8B2A9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Wedge protein 1 (gp024)
J, M
285Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE8B2H1 (Escherichia phage JohannRWettstein)
Explore A0AAE8B2H1 
Go to UniProtKB:  A0AAE8B2H1
Entity Groups
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UniProt GroupA0AAE8B2H1
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Spacer protein (gp019)
N, O
113Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE7VUR9 (Escherichia phage JohannRWettstein)
Explore A0AAE7VUR9 
Go to UniProtKB:  A0AAE7VUR9
Entity Groups
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UniProt GroupA0AAE7VUR9
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Reference Sequence
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|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
LTF platform protein (gp025)100Escherichia phage JohannRWettsteinMutation(s): 0 
UniProt
Find proteins for A0AAE8B758 (Escherichia phage JohannRWettstein)
Explore A0AAE8B758 
Go to UniProtKB:  A0AAE8B758
Entity Groups
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UniProt GroupA0AAE8B758
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Agriculture, Forestry and Fisheries (MAFF)JapanGD0696J004
Japan Society for the Promotion of Science (JSPS)Japan21K20645

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release