8JYS

SARS-CoV-2 Spike RBD (dimer) in complex with two 2S-1244 nanobodies

PDB DOI: https://doi.org/10.2210/pdb8JYS/pdb
EM Map EMD-36730: EMDB EMDataResource

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

Deposited: 2023-07-03 Released: 2024-06-12
Deposition Author(s): Yang, Y., Zhang, C.H.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

A novel nanobody broadly neutralizes SARS-CoV-2 via induction of spike trimer dimers conformation

Yang, Y., Zhang, J., Zhang, S., Zhang, C., Shen, C., Song, S., Wang, Y., Peng, Y., Gong, X., Dai, J., Xie, C., Khrustaleva, T.A., Khrustalev, V.V., Huo, Y., Lu, D., Yao, D., Zhao, J., Liu, Y., Lu, H.

(2023) Exploration : 20230086

DOI: https://doi.org/10.1002/EXP.20230086

Macromolecule Content

Total Structure Weight: 75.42 kDa
Atom Count: 3,522
Modelled Residue Count: 441
Deposited Residue Count: 676
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IBT-CoV144 nanobody	A, C	142	Camelus bactrianus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B, D	196	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release

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 R01GM133198.