7WK0

Local refine of Omicron spike bitrimer with 6m6 antibody

PDB DOI: https://doi.org/10.2210/pdb7WK0/pdb
EM Map EMD-32554: EMDB EMDataResource

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

Deposited: 2022-01-08 Released: 2022-07-13
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding.

Wang, Y., Zhan, W., Liu, J., Wang, Y., Zhang, X., Zhang, M., Han, L., Ma, Y., Lu, L., Wen, Y., Chen, Z., Zhao, J., Wu, F., Sun, L., Huang, J.

(2022) Cell Res 32: 862-865

PubMed: 35768499 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00684-0
Primary Citation of Related Structures:
7WJY, 7WJZ, 7WK0

Organizational Affiliation

Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 139.33 kDa
Atom Count: 9,724
Modelled Residue Count: 1,264
Deposited Residue Count: 1,276
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 heavy chain	A, D	226	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 light chain	B, E	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, F	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain 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 Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth F] MOL2 format, chain G [auth C] MOL2 format, chain H [auth F] mmCIF format, chain G [auth C] mmCIF format, chain H [auth F]	G [auth C], H [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth C] Focus chain H [auth F] Interactions & Density Focus chain G [auth C] Focus chain H [auth F]