7WJZ

Omicron Spike bitrimer with 6m6 antibody

PDB DOI: https://doi.org/10.2210/pdb7WJZ/pdb
EM Map EMD-32553: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
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: 3.34 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: 1,148.16 kDa
Atom Count: 69,158
Modelled Residue Count: 8,886
Deposited Residue Count: 10,356
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B] D [auth I] G [auth J] J [auth K] M [auth L] A [auth B], D [auth I], G [auth J], J [auth K], M [auth L], P [auth M]	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 39 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: 8	Glycosylation Focus chain A [auth B] Focus chain D [auth I] Focus chain G [auth J] Focus chain J [auth K] Focus chain M [auth L] Focus chain P [auth M]	Go to GlyGen: P0DTC2-1
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 heavy chain	B [auth A] E [auth D] H [auth E] K [auth F] N [auth G] B [auth A], E [auth D], H [auth E], K [auth F], N [auth G], Q [auth H]	227	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
6m6 light chain	C F [auth N] I [auth O] L [auth P] O [auth Q] C, F [auth N], I [auth O], L [auth P], O [auth Q], R	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 AA [auth I] SDF format, chain AB [auth L] SDF format, chain BA [auth I] SDF format, chain BB [auth L] SDF format, chain CA [auth I] SDF format, chain CB [auth L] SDF format, chain DA [auth I] SDF format, chain DB [auth L] SDF format, chain EA [auth I] SDF format, chain EB [auth L] SDF format, chain FA [auth I] SDF format, chain FB [auth M] SDF format, chain GA [auth I] SDF format, chain GB [auth M] SDF format, chain HA [auth J] SDF format, chain HB [auth M] SDF format, chain IA [auth J] SDF format, chain IB [auth M] SDF format, chain JA [auth J] SDF format, chain JB [auth M] SDF format, chain KA [auth J] SDF format, chain KB [auth M] SDF format, chain LA [auth J] SDF format, chain LB [auth M] SDF format, chain MA [auth J] SDF format, chain MB [auth M] SDF format, chain NA [auth J] SDF format, chain NB [auth M] SDF format, chain OA [auth J] SDF format, chain OB [auth M] SDF format, chain PA [auth K] SDF format, chain QA [auth K] SDF format, chain RA [auth K] SDF format, chain S [auth B] SDF format, chain SA [auth K] SDF format, chain T [auth B] SDF format, chain TA [auth K] SDF format, chain U [auth B] SDF format, chain UA [auth K] SDF format, chain V [auth B] SDF format, chain VA [auth K] SDF format, chain W [auth B] SDF format, chain WA [auth L] SDF format, chain X [auth B] SDF format, chain XA [auth L] SDF format, chain Y [auth B] SDF format, chain YA [auth L] SDF format, chain Z [auth I] SDF format, chain ZA [auth L] MOL2 format, chain AA [auth I] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth I] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth I] MOL2 format, chain CB [auth L] MOL2 format, chain DA [auth I] MOL2 format, chain DB [auth L] MOL2 format, chain EA [auth I] MOL2 format, chain EB [auth L] MOL2 format, chain FA [auth I] MOL2 format, chain FB [auth M] MOL2 format, chain GA [auth I] MOL2 format, chain GB [auth M] MOL2 format, chain HA [auth J] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth J] MOL2 format, chain IB [auth M] MOL2 format, chain JA [auth J] MOL2 format, chain JB [auth M] MOL2 format, chain KA [auth J] MOL2 format, chain KB [auth M] MOL2 format, chain LA [auth J] MOL2 format, chain LB [auth M] MOL2 format, chain MA [auth J] MOL2 format, chain MB [auth M] MOL2 format, chain NA [auth J] MOL2 format, chain NB [auth M] MOL2 format, chain OA [auth J] MOL2 format, chain OB [auth M] MOL2 format, chain PA [auth K] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth K] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth L] MOL2 format, chain Z [auth I] MOL2 format, chain ZA [auth L] mmCIF format, chain AA [auth I] mmCIF format, chain AB [auth L] mmCIF format, chain BA [auth I] mmCIF format, chain BB [auth L] mmCIF format, chain CA [auth I] mmCIF format, chain CB [auth L] mmCIF format, chain DA [auth I] mmCIF format, chain DB [auth L] mmCIF format, chain EA [auth I] mmCIF format, chain EB [auth L] mmCIF format, chain FA [auth I] mmCIF format, chain FB [auth M] mmCIF format, chain GA [auth I] mmCIF format, chain GB [auth M] mmCIF format, chain HA [auth J] mmCIF format, chain HB [auth M] mmCIF format, chain IA [auth J] mmCIF format, chain IB [auth M] mmCIF format, chain JA [auth J] mmCIF format, chain JB [auth M] mmCIF format, chain KA [auth J] mmCIF format, chain KB [auth M] mmCIF format, chain LA [auth J] mmCIF format, chain LB [auth M] mmCIF format, chain MA [auth J] mmCIF format, chain MB [auth M] mmCIF format, chain NA [auth J] mmCIF format, chain NB [auth M] mmCIF format, chain OA [auth J] mmCIF format, chain OB [auth M] mmCIF format, chain PA [auth K] mmCIF format, chain QA [auth K] mmCIF format, chain RA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth K] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth K] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth K] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth L] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth L] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth L] mmCIF format, chain Z [auth I] mmCIF format, chain ZA [auth L]	AA [auth I] AB [auth L] BA [auth I] BB [auth L] CA [auth I] AA [auth I], AB [auth L], BA [auth I], BB [auth L], CA [auth I], CB [auth L], DA [auth I], DB [auth L], EA [auth I], EB [auth L], FA [auth I], FB [auth M], GA [auth I], GB [auth M], HA [auth J], HB [auth M], IA [auth J], IB [auth M], JA [auth J], JB [auth M], KA [auth J], KB [auth M], LA [auth J], LB [auth M], MA [auth J], MB [auth M], NA [auth J], NB [auth M], OA [auth J], OB [auth M], PA [auth K], QA [auth K], RA [auth K], S [auth B], SA [auth K], T [auth B], TA [auth K], U [auth B], UA [auth K], V [auth B], VA [auth K], W [auth B], WA [auth L], X [auth B], XA [auth L], Y [auth B], YA [auth L], Z [auth I], ZA [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth I] Focus chain AB [auth L] Focus chain BA [auth I] Focus chain BB [auth L] Focus chain CA [auth I] Focus chain CB [auth L] Focus chain DA [auth I] Focus chain DB [auth L] Focus chain EA [auth I] Focus chain EB [auth L] Focus chain FA [auth I] Focus chain FB [auth M] Focus chain GA [auth I] Focus chain GB [auth M] Focus chain HA [auth J] Focus chain HB [auth M] Focus chain IA [auth J] Focus chain IB [auth M] Focus chain JA [auth J] Focus chain JB [auth M] Focus chain KA [auth J] Focus chain KB [auth M] Focus chain LA [auth J] Focus chain LB [auth M] Focus chain MA [auth J] Focus chain MB [auth M] Focus chain NA [auth J] Focus chain NB [auth M] Focus chain OA [auth J] Focus chain OB [auth M] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain WA [auth L] Focus chain X [auth B] Focus chain XA [auth L] Focus chain Y [auth B] Focus chain YA [auth L] Focus chain Z [auth I] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth I] Focus chain AB [auth L] Focus chain BA [auth I] Focus chain BB [auth L] Focus chain CA [auth I] Focus chain CB [auth L] Focus chain DA [auth I] Focus chain DB [auth L] Focus chain EA [auth I] Focus chain EB [auth L] Focus chain FA [auth I] Focus chain FB [auth M] Focus chain GA [auth I] Focus chain GB [auth M] Focus chain HA [auth J] Focus chain HB [auth M] Focus chain IA [auth J] Focus chain IB [auth M] Focus chain JA [auth J] Focus chain JB [auth M] Focus chain KA [auth J] Focus chain KB [auth M] Focus chain LA [auth J] Focus chain LB [auth M] Focus chain MA [auth J] Focus chain MB [auth M] Focus chain NA [auth J] Focus chain NB [auth M] Focus chain OA [auth J] Focus chain OB [auth M] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain WA [auth L] Focus chain X [auth B] Focus chain XA [auth L] Focus chain Y [auth B] Focus chain YA [auth L] Focus chain Z [auth I] Focus chain ZA [auth L]