7E5S

SARS-CoV-2 S trimer with four-antibody cocktail complex

PDB DOI: https://doi.org/10.2210/pdb7E5S/pdb
EM Map EMD-30994: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Mammalian expression vector BsrGI-MCS-pcDNA3.1
Mutation(s): Yes

Deposited: 2021-02-20 Released: 2021-11-17
Deposition Author(s): Sun, Y., Wang, L., Wang, N., Feng, R., Wang, X.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 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

Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms.

Sun, Y., Wang, L., Feng, R., Wang, N., Wang, Y., Zhu, D., Xing, X., Yang, P., Zhang, Y., Li, W., Wang, X.

(2021) Cell Res 31: 597-600

PubMed: 33782529 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00497-7
Primary Citation of Related Structures:
7E5R, 7E5S

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: 682.39 kDa
Atom Count: 38,916
Modelled Residue Count: 5,038
Deposited Residue Count: 6,186
Unique protein chains: 9

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,281	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: 3	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
H014 light chain	D, F [auth H]	210	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H014 heavy chain	E, J [auth L]	223	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P17 heavy chain	G [auth I], H [auth J]	120	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
P17 light chain	I [auth K], Q [auth T]	108	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
FC05 light chain	K [auth N], N [auth Q], P [auth S]	109	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
HB27 light chain	L [auth O]	111	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
FC05 heavy chain	M [auth P], R [auth U], S [auth V]	120	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
HB27 heavy chain	O [auth R]	223	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 10
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], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], T [auth F], U [auth G], V [auth M], 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 EA [auth e] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth M] 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 EA [auth e] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth M] Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT