7WP0

Cryo-EM structure of SARS-CoV-2 Delta S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)

PDB DOI: https://doi.org/10.2210/pdb7WP0/pdb
EM Map EMD-32665: EMDB EMDataResource

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

Deposited: 2022-01-22 Released: 2022-07-20
Deposition Author(s): Zheng, Q., Sun, H., Ju, B., Zhang, Z., Li, S., Xia, N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209.

Ju, B., Zheng, Q., Guo, H., Fan, Q., Li, T., Song, S., Sun, H., Shen, S., Zhou, X., Xue, W., Cui, L., Zhou, B., Li, S., Xia, N., Zhang, Z.

(2022) Cell Res 32: 491-494

PubMed: 35260792 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00638-6
Primary Citation of Related Structures:
7WON, 7WP0, 7WP1, 7WP2, 7WP5

Organizational Affiliation

Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China. jubin2013@163.com.

Macromolecule Content

Total Structure Weight: 47.61 kDa
Atom Count: 3,174
Modelled Residue Count: 407
Deposited Residue Count: 431
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG c335_light_IGLV1-40_IGLJ3	A [auth L]	111	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A5C2GQT9 (Homo sapiens) Explore A0A5C2GQT9 Go to UniProtKB: A0A5C2GQT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5C2GQT9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VacW-209 heavy chain	B [auth H]	131	Homo sapiens	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth F]	189	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth F]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth F] MOL2 format, chain D [auth F] mmCIF format, chain D [auth F]	D [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth F] Interactions & Density Focus chain D [auth F]