7WTF | pdb_00007wtf

SARS-CoV-2 Omicron variant spike in complex with Fab XGv051

PDB DOI: https://doi.org/10.2210/pdb7WTF/pdb
EM Map EMD-32784: 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: 2022-02-04 Released: 2022-12-14
Deposition Author(s): Wang, X., Fu, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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

Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.

Wang, L., Fu, W., Bao, L., Jia, Z., Zhang, Y., Zhou, Y., Wu, W., Wu, J., Zhang, Q., Gao, Y., Wang, K., Wang, Q., Qin, C., Wang, X.

(2022) Cell Res 32: 691-694

PubMed: 35672388 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00677-z
Primary Citation of Related Structures:
7WTF, 7WTG, 7WTH, 7WTI, 7WTJ, 7WTK

Organizational Affiliation

CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 472.24 kDa
Atom Count: 32,049
Modeled Residue Count: 3,966
Deposited Residue Count: 4,119
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of XGv051	A [auth H], F [auth G], H [auth I]	120	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
Light chain of XGv051	B [auth L], G [auth J], I [auth K]	104	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 glycoprotein	C [auth B], D [auth C], E [auth D]	1,149	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 36 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: 16	Glycosylation Focus chain C [auth B] Focus chain D [auth C] Focus chain E [auth D]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], J [auth A], K [auth E], N, BA [auth b], CA [auth c], J [auth A], K [auth E], N, O, P, Q, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J [auth A] Focus chain K [auth E] Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J [auth A] Focus chain K [auth E] Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], L [auth F], M, R, S	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain L [auth F] Focus chain M Focus chain R Focus chain S Interactions & Density Focus chain AA [auth a] Focus chain L [auth F] Focus chain M Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AB [auth D] BB [auth D] CB [auth D] DA [auth B] DB [auth D] AB [auth D], BB [auth D], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D]