7CWS

SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail

PDB DOI: https://doi.org/10.2210/pdb7CWS/pdb
EM Map EMD-30486: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-08-31 Released: 2020-12-16
Deposition Author(s): Wang, L., Wang, X.

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 1.2 of the entry. See complete history.

Literature

Structure-based development of human antibody cocktails against SARS-CoV-2.

Wang, N., Sun, Y., Feng, R., Wang, Y., Guo, Y., Zhang, L., Deng, Y.Q., Wang, L., Cui, Z., Cao, L., Zhang, Y.J., Li, W., Zhu, F.C., Qin, C.F., Wang, X.

(2021) Cell Res 31: 101-103

PubMed: 33262454 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-020-00446-w
Primary Citation of Related Structures:
7CWS, 7CWT, 7CWU

Organizational Affiliation

CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 536.49 kDa
Atom Count: 36,389
Modelled Residue Count: 4,602
Deposited Residue Count: 4,776
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of FC05 Fab	A [auth L], I [auth N], K [auth P]	120	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of FC05 Fab	B [auth C], J [auth K], L [auth M]	109	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of H014 Fab	C [auth D], E [auth F], G [auth H]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of H014 Fab	D [auth E], F [auth G], H [auth I]	122	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	M [auth O], N [auth Q], O [auth R]	1,134	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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: 10	Glycosylation Focus chain M [auth O] Focus chain N [auth Q] Focus chain O [auth R]	Go to GlyGen: P0DTC2-1
Sequence AnnotationsExpand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], P [auth A], AA [auth a], BA [auth b], CA [auth c], DA [auth d], P [auth A], Q [auth B], R [auth J], S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth J] Focus chain S 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 AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth J] Focus chain S 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

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 RA [auth R] SDF format, chain EA [auth O] SDF format, chain FA [auth O] SDF format, chain GA [auth O] SDF format, chain HA [auth O] SDF format, chain IA [auth O] SDF format, chain JA [auth Q] SDF format, chain KA [auth Q] SDF format, chain LA [auth Q] SDF format, chain MA [auth Q] SDF format, chain NA [auth Q] SDF format, chain OA [auth Q] SDF format, chain PA [auth R] SDF format, chain QA [auth R] SDF format, chain SA [auth R] SDF format, chain TA [auth R] MOL2 format, chain RA [auth R] MOL2 format, chain EA [auth O] MOL2 format, chain FA [auth O] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth O] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth Q] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth Q] MOL2 format, chain MA [auth Q] MOL2 format, chain NA [auth Q] MOL2 format, chain OA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth R] MOL2 format, chain SA [auth R] MOL2 format, chain TA [auth R] mmCIF format, chain RA [auth R] mmCIF format, chain EA [auth O] mmCIF format, chain FA [auth O] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth O] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth Q] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth Q] mmCIF format, chain MA [auth Q] mmCIF format, chain NA [auth Q] mmCIF format, chain OA [auth Q] mmCIF format, chain PA [auth R] mmCIF format, chain QA [auth R] mmCIF format, chain SA [auth R] mmCIF format, chain TA [auth R]	EA [auth O] FA [auth O] GA [auth O] HA [auth O] IA [auth O] EA [auth O], FA [auth O], GA [auth O], HA [auth O], IA [auth O], JA [auth Q], KA [auth Q], LA [auth Q], MA [auth Q], NA [auth Q], OA [auth Q], PA [auth R], QA [auth R], RA [auth R], SA [auth R], TA [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth O] Focus chain FA [auth O] Focus chain GA [auth O] Focus chain HA [auth O] Focus chain IA [auth O] Focus chain JA [auth Q] Focus chain KA [auth Q] Focus chain LA [auth Q] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth R] Focus chain RA [auth R] Focus chain SA [auth R] Focus chain TA [auth R] Interactions & Density Focus chain EA [auth O] Focus chain FA [auth O] Focus chain GA [auth O] Focus chain HA [auth O] Focus chain IA [auth O] Focus chain JA [auth Q] Focus chain KA [auth Q] Focus chain LA [auth Q] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth R] Focus chain RA [auth R] Focus chain SA [auth R] Focus chain TA [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Wang, L.

Wang, X.

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2021-01-13
Changes: Database references
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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7CWS

SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail

Structure-based development of human antibody cocktails against SARS-CoV-2.

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)