7YEG

SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2

PDB DOI: https://doi.org/10.2210/pdb7YEG/pdb
EM Map EMD-33772: 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: 2022-07-05 Released: 2022-08-24
Deposition Author(s): Liu, B., Gao, X., Li, Z., Chen, X., He, J., Chen, L., Xiong, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.73 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.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7YDI

Macromolecule Content

Total Structure Weight: 758.18 kDa
Atom Count: 49,974
Modelled Residue Count: 6,306
Deposited Residue Count: 6,741
Unique protein chains: 4

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	1,208	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	D [auth E], I [auth J], J [auth M]	597	Homo sapiens	Mutation(s): 0 Gene Names: ACE2 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of R1-32 Fab	E [auth H], G, K [auth N]	228	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
light chain of R1-32 Fab	F [auth L], H [auth I], L [auth O]	214	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth D], N [auth F], O [auth K], P, Q, M [auth D], N [auth F], O [auth K], P, Q, R	2		N-Glycosylation	Interactions Focus chain M [auth D] Focus chain N [auth F] Focus chain O [auth K] Focus chain P Focus chain Q Focus chain R Interactions & Density Focus chain M [auth D] Focus chain N [auth F] Focus chain O [auth K] Focus chain P Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain BB [auth M] SDF format, chain CA [auth B] SDF format, chain CB [auth M] SDF format, chain DA [auth B] SDF format, chain DB [auth M] SDF format, chain EA [auth B] SDF format, chain EB [auth M] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] 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 RA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain T [auth A] SDF format, chain TA [auth E] SDF format, chain U [auth A] SDF format, chain UA [auth E] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth J] SDF format, chain X [auth A] SDF format, chain XA [auth J] SDF format, chain Y [auth A] SDF format, chain YA [auth J] SDF format, chain Z [auth A] SDF format, chain ZA [auth J] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth M] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth M] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth M] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] 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 RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth J] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth J]	AA [auth B] BA [auth B] BB [auth M] CA [auth B] CB [auth M] AA [auth B], BA [auth B], BB [auth M], CA [auth B], CB [auth M], DA [auth B], DB [auth M], EA [auth B], EB [auth M], FA [auth B], GA [auth B], HA [auth B], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], RA [auth E], S [auth A], SA [auth E], T [auth A], TA [auth E], U [auth A], UA [auth E], V [auth A], W [auth A], WA [auth J], X [auth A], XA [auth J], Y [auth A], YA [auth J], Z [auth A], ZA [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth M] Focus chain CA [auth B] Focus chain CB [auth M] Focus chain DA [auth B] Focus chain DB [auth M] Focus chain EA [auth B] Focus chain EB [auth M] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] 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 RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth J] Focus chain X [auth A] Focus chain XA [auth J] Focus chain Y [auth A] Focus chain YA [auth J] Focus chain Z [auth A] Focus chain ZA [auth J] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth M] Focus chain CA [auth B] Focus chain CB [auth M] Focus chain DA [auth B] Focus chain DB [auth M] Focus chain EA [auth B] Focus chain EB [auth M] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] 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 RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth J] Focus chain X [auth A] Focus chain XA [auth J] Focus chain Y [auth A] Focus chain YA [auth J] Focus chain Z [auth A] Focus chain ZA [auth J]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain QA [auth E] SDF format, chain VA [auth J] MOL2 format, chain AB [auth M] MOL2 format, chain QA [auth E] MOL2 format, chain VA [auth J]	AB [auth M], QA [auth E], VA [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth M] Focus chain QA [auth E] Focus chain VA [auth J] Interactions & Density Focus chain AB [auth M] Focus chain QA [auth E] Focus chain VA [auth J]