7E9N | pdb_00007e9n

Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 down RBD, state1)

PDB DOI: https://doi.org/10.2210/pdb7E9N/pdb
EM Map EMD-31033: 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: 2021-03-04 Released: 2022-04-06
Deposition Author(s): Wang, X.F., Zhu, Y.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD

Wang, X., Hu, A., Chen, X., Zhang, Y., Yu, F., Yue, S., Li, A., Zhang, J., Pan, Z., Yang, Y., Lin, Y., Gao, L., Zhou, J., Zhao, J., Li, F., Shi, Y., Huang, F., Yang, X., Peng, Y., Tu, L., Zhang, H., Zheng, H., He, J., Zhang, H., Xu, L., Huang, Q., Zhu, Y., Deng, K., Ye, L.

(2022) Signal Transduct Target Ther 7: 114

DOI: https://doi.org/10.1038/s41392-022-00954-8

Macromolecule Content

Total Structure Weight: 525.26 kDa
Atom Count: 33,519
Modeled Residue Count: 4,313
Deposited Residue Count: 4,728
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth A], C	1,121	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A [auth B] Focus chain B [auth A] Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 35B5 Fab	D [auth O], F [auth X], H [auth L]	218	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 35B5 Fab	E [auth P], G [auth Y], I [auth H]	237	Homo sapiens	Mutation(s): 0

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 C] SDF format, chain CA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain M [auth B] SDF format, chain JA [auth C] SDF format, chain J [auth B] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain M [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain M [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	AA [auth A] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth A], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], J [auth B], JA [auth C], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth A], T [auth A], 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 C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth B] Focus chain JA [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth A] Focus chain T [auth A] 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 C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth B] Focus chain JA [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth A] Focus chain T [auth A] 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]