9UT0 | pdb_00009ut0

Cryo-EM structure of A17(1-16) peptide-bound D13 assembled into scaffold-like particles from vaccinia virus

PDB DOI: https://doi.org/10.2210/pdb9UT0/pdb
EM Map EMD-64477: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Orthopoxvirus vaccinia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-02 Released: 2026-08-05
Deposition Author(s): Jang, Y.T., Kim, S.M., Lee, S.N., Ryu, B.H., Jeong, H.S., Kang, E.S., Sul, J.H., Kim, Y.H., Jo, D.G., Hyun, J.K.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UT0

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

Literature

Structures of in vitro assembly products of poxvirus scaffolding protein reveal transition from pre-assembly state to fully assembled scaffold

Jang, Y.T., Kim, S.M., Lee, S.N., Ryu, B.H., Jeong, H.S., Kang, E.S., Sul, J.H., Kim, Y.H., Jo, D.G., Hyun, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 1,115.07 kDa
Atom Count: 75,780
Modeled Residue Count: 9,522
Deposited Residue Count: 9,918
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scaffold protein OPG125	A B C D E A, B, C, D, E, F, G [auth H], H [auth G], I, J [auth K], K [auth L], L [auth J], M [auth N], N [auth M], O, P [auth R], Q, R [auth P]	551	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG125, VACWR118, D13L
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve)) Explore P68440 Go to UniProtKB: P68440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68440
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2026-08-05
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.