32YY | pdb_000032yy

Cryo-EM structure of native, mature HERV-K pentameric capsomer

PDB DOI: https://doi.org/10.2210/pdb32YY/pdb
EM Map EMD-59279: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human endogenous retrovirus K
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-08-02 Released: 2026-08-19
Deposition Author(s): Lyu, C., Shen, Y., Zhang, P.
Funding Organization(s): Wellcome Trust, Chinese Scholarship Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 32YY

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

Literature

Structural Insights into Native, Mature Human Endogenous Retrovirus K (HERV-K) Capsids

Lyu, C., Peeples, C.A., Zhang, Z., Shen, Y., Hou, Z., Harding, E.F., Hope, J., Perilla, J.R., Katzourakis, A., Zhang, P.

To be published.

Macromolecule Content

Total Structure Weight: 131.59 kDa
Atom Count: 8,886
Modeled Residue Count: 1,125
Deposited Residue Count: 1,175
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endogenous retrovirus group K member 8 Gag polyprotein	A, B, C, D, E	235	Human endogenous retrovirus K	Mutation(s): 0 Gene Names: ERVK-8
UniProt
Find proteins for P62685 (Homo sapiens) Explore P62685 Go to UniProtKB: P62685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP (Subject of Investigation/LOI) Query on IHP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	311427/Z/24/Z
Chinese Scholarship Council	China	CNR00051

Revision History (Full details and data files)

Version 1.0: 2026-08-19
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.