9KZJ | pdb_00009kzj

Cryo-EM structure of bacteriophage T1 capsid

• PDB DOI: https://doi.org/10.2210/pdb9KZJ/pdb
• EM Map EMD-62664: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage T1
• Mutation(s): No 


• Deposited: 2024-12-10 Released: 2025-03-12 
• Deposition Author(s): Chen, Y., Liu, H.R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The in situ structure of T-series T1 reveals a conserved Lambda-like tail tip

Chen, Y., Liu, H.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A7B6C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 14-mer - A7B7 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 376.04 kDa 
• Atom Count: 24,095 
• Modelled Residue Count: 3,145 
• Deposited Residue Count: 3,436 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D, E, F, G	319	Escherichia phage T1	Mutation(s): 0
UniProt
Find proteins for Q6XQD3 (Escherichia phage T1) Explore Q6XQD3  Go to UniProtKB:  Q6XQD3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cement protein II	H [auth N], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M]	158	Escherichia phage T1	Mutation(s): 0
UniProt
Find proteins for Q6XQD5 (Escherichia phage T1) Explore Q6XQD5  Go to UniProtKB:  Q6XQD5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BIG2 domain-containing protein	I [auth H]	255	Escherichia phage T1	Mutation(s): 0
UniProt
Find proteins for Q6XQD4 (Escherichia phage T1) Explore Q6XQD4  Go to UniProtKB:  Q6XQD4

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Chen, Y., Liu, H.R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	12034006
National Natural Science Foundation of China (NSFC)	China	32430020
National Natural Science Foundation of China (NSFC)	China	32071209

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release