7E5R

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

PDB DOI: https://doi.org/10.2210/pdb7E5R/pdb
EM Map EMD-30993: EMDB EMDataResource

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

Deposited: 2021-02-20 Released: 2021-10-13
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: 719.9 kDa
Atom Count: 40,683
Modelled Residue Count: 5,262
Deposited Residue Count: 6,513
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H014 light chain	A [auth H], C [auth D], E	210	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H014 heavy chain	B [auth L], D [auth N], F [auth O]	223	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
Spike glycoprotein	G [auth A], N [auth B], U [auth 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: 5	Glycosylation Focus chain G [auth A] Focus chain N [auth B] Focus chain U [auth C]	Go to GlyGen: P0DTC2-1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P17 heavy chain	H [auth M], J [auth T], L [auth I]	120	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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 U], K [auth V], M [auth K]	108	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
FC05 light chain	O [auth R], Q [auth S], S [auth Q]	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
FC05 heavy chain	P [auth W], R [auth X], T [auth P]	120	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 8
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], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], V [auth F], W [auth G], X [auth J], 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 FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth J] 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 FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth J] Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT