7Y7J

SARS-CoV-2 S trimer in complex with 1F Fab

PDB DOI: https://doi.org/10.2210/pdb7Y7J/pdb
EM Map EMD-33667: 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: 2022-06-22 Released: 2023-02-22
Deposition Author(s): Zhao, S., Liu, F., Yang, X., Zhong, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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 core epitope targeting antibody of SARS-CoV-2.

Zhao, S., Liu, F., Qiu, S., Lan, Q., Wu, Y., Xu, W., Ke, J., Yang, J., Liu, X., Wang, K., Guo, H., Xia, S., Zhang, F., Wang, J., Hu, X., Lu, L., Jiang, S., Zhao, S., Liu, L., Xie, Y., Yang, X., Wang, H., Zhong, G.

(2023) Protein Cell 14: 74-78

PubMed: 36726762 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/procel/pwac042
Primary Citation of Related Structures:
7Y7J, 7Y7K

Organizational Affiliation

iHuman Institute, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content

Total Structure Weight: 465.32 kDa
Atom Count: 23,742
Modelled Residue Count: 3,191
Deposited Residue Count: 4,107
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	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 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: 13	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1F VH	D [auth E]	132	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
1F VL	E [auth D]	111	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	F, G, H, I, J, F, G, H, I, J, K, L, M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T], T [auth U]	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T] Focus chain T [auth U] Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T] Focus chain T [auth U]
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 A] SDF format, chain BA [auth A] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] 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 C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] 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 U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] 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 C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] 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 U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] 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 C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] 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 U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth B] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] 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 JA [auth B] Focus chain KA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] 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 U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] 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 JA [auth B] Focus chain KA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] 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 U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]