9ZBI | pdb_00009zbi

The cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration protein)

PDB DOI: https://doi.org/10.2210/pdb9ZBI/pdb
EM Map EMD-73989: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pakpunavirus
Mutation(s): No

Deposited: 2025-11-20 Released: 2026-04-15
Deposition Author(s): Li, F., Cingolani, G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZBI

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

Literature

The cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration protein)

Li, F., Cingolani, G.

To be published.

Macromolecule Content

Total Structure Weight: 281.12 kDa
Atom Count: 19,323
Modeled Residue Count: 2,409
Deposited Residue Count: 2,472
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D, E A, B, C, D, E, F	344	Pakpunavirus	Mutation(s): 0
UniProt
Find proteins for A0A9Y1CF61 (Pseudomonas phage vB_Paer_Ps12) Explore A0A9Y1CF61 Go to UniProtKB: A0A9Y1CF61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9Y1CF61
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Decorating protein	G, H, I	136	Pakpunavirus	Mutation(s): 0
UniProt
Find proteins for A0A4Y6EA47 (Pseudomonas phage vB_PaM_EPA1) Explore A0A4Y6EA47 Go to UniProtKB: A0A4Y6EA47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Y6EA47
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM140733

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.