9ZBS | pdb_00009zbs

The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)

PDB DOI: https://doi.org/10.2210/pdb9ZBS/pdb
EM Map EMD-73999: EMDB EMDataResource

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

Deposited: 2025-11-21 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: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZBS

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

Literature

The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)

Li, F., Cingolani, G.

To be published.

Macromolecule Content

Total Structure Weight: 1,084.11 kDa
Atom Count: 72,366
Modeled Residue Count: 9,006
Deposited Residue Count: 9,522
Unique protein chains: 4

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	479	Pakpunavirus	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Head to Tail protein gp72	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	158	Pakpunavirus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Head-tail joining protein	AA [auth a] BA [auth b] CA [auth c] DA [auth d] Y AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	126	Pakpunavirus	Mutation(s): 0

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail completion protein	EA [auth e] FA [auth f] GA [auth g] HA [auth h] IA [auth i] EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j]	187	Pakpunavirus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 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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View more in-depth experimental data

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.