7YD1 | pdb_00007yd1

Local refinement of SARS-CoV-2 Omicron S trimer complexed with XG005

PDB DOI: https://doi.org/10.2210/pdb7YD1/pdb
EM Map EMD-33745: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-07-02 Released: 2023-07-12
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7YD1

This is version 1.2 of the entry. See complete history.

Literature

OS-XG005

Zhan, W.Q., Zhang, X.

To be published.

Macromolecule Content

Total Structure Weight: 47.01 kDa
Atom Count: 3,305
Modeled Residue Count: 428
Deposited Residue Count: 428
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth C]	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
XG005-VH	B [auth A]	122	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
XG005-VL	C [auth B]	108	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC2302500

Revision History (Full details and data files)

Version 1.0: 2023-07-12
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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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.