7WT7

SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1)

PDB DOI: https://doi.org/10.2210/pdb7WT7/pdb
EM Map EMD-32770: EMDB EMDataResource

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

Deposited: 2022-02-04 Released: 2023-06-07
Deposition Author(s): Wang, X., Wang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.

Liu, S., Jia, Z., Nie, J., Liang, Z., Xie, J., Wang, L., Zhang, L., Wang, X., Wang, Y., Huang, W.

(2022) Cell Discov 8: 81-81

PubMed: 35977939 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00443-w
Primary Citation of Related Structures:
7WT7, 7WT8, 7WT9

Organizational Affiliation

Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.

Macromolecule Content

Total Structure Weight: 459.58 kDa
Atom Count: 28,322
Modelled Residue Count: 3,523
Deposited Residue Count: 4,039
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, B, C	1,270	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 38 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: 14	Glycosylation Focus chain A Focus chain B Focus chain C	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
Heavy chain of Fab 9A8	D [auth H]	122	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
Light chain of Fab 9A8	E [auth D]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
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	F [auth E]	3		N-Glycosylation	Interactions Focus chain F [auth E] Interactions & Density Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F], H [auth G], I	2		N-Glycosylation	Interactions Focus chain G [auth F] Focus chain H [auth G] Focus chain I Interactions & Density Focus chain G [auth F] Focus chain H [auth G] Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CA [auth B] SDF format, chain GA [auth B] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain QA [auth C] SDF format, chain S [auth A] SDF format, chain TA [auth C] SDF format, chain VA [auth C] SDF format, chain XA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain XA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain XA [auth C]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]