7YC2 | pdb_00007yc2

Crystal structure of auxiliary protein in complex with human protein

PDB DOI: https://doi.org/10.2210/pdb7YC2/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-30 Released: 2023-12-06
Deposition Author(s): Gao, X., Cui, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.250 (Depositor), 0.244 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YC2

This is version 1.3 of the entry. See complete history.

Literature

SARS-CoV-2 ORF10 hijacking ubiquitination machinery reveals potential unique drug targeting sites

Zhu, K., Song, L., Wang, L., Hua, L., Luo, Z., Wang, T., Qin, B., Yuan, S., Gao, X., Mi, W., Cui, S.

(2024) Acta Pharm Sin B

DOI: https://doi.org/10.1016/j.apsb.2024.05.018

Macromolecule Content

Total Structure Weight: 113.35 kDa
Atom Count: 7,885
Modeled Residue Count: 979
Deposited Residue Count: 988
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein zyg-11 homolog B	A, B, C, D	240	Homo sapiens	Mutation(s): 0 Gene Names: ZYG11B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0D3 (Homo sapiens) Explore Q9C0D3 Go to UniProtKB: Q9C0D3
PHAROS: Q9C0D3 GTEx: ENSG00000162378
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C0D3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF	E, F, G, H	7	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A663DJA2 (Severe acute respiratory syndrome coronavirus 2) Explore A0A663DJA2 Go to UniProtKB: A0A663DJA2
Entity Groups
UniProt Group	A0A663DJA2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.250 (Depositor), 0.244 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.3	α = 90
b = 72.8	β = 113.4
c = 127.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release
Version 1.1: 2024-06-19
Changes: Database references
Version 1.2: 2024-10-16
Changes: Structure summary
Version 1.3: 2026-03-04
Changes: Refinement description