8DLP

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2

PDB DOI: https://doi.org/10.2210/pdb8DLP/pdb
EM Map EMD-27509: EMDB EMDataResource

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

Deposited: 2022-07-08 Released: 2022-08-31
Deposition Author(s): Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S.
Funding Organization(s): Canada Excellence Research Chair Award, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 655.56 kDa
Atom Count: 40,095
Modelled Residue Count: 4,908
Deposited Residue Count: 5,682
Unique protein chains: 2

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	1,288	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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	D, E, F	606	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885
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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	2	N/A	N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
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 AA [auth A] SDF format, chain CB [auth E] SDF format, chain EB [auth E] SDF format, chain GA [auth B] SDF format, chain GB [auth E] SDF format, chain HB [auth E] SDF format, chain KA [auth B] SDF format, chain LB [auth F] SDF format, chain OA [auth C] SDF format, chain QA [auth C] SDF format, chain SA [auth C] SDF format, chain WA [auth D] SDF format, chain AB [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth D] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth E] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth E] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain IB [auth F] SDF format, chain JA [auth B] SDF format, chain JB [auth F] SDF format, chain KB [auth F] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain MB [auth F] SDF format, chain NA [auth B] SDF format, chain NB [auth F] SDF format, chain PA [auth C] SDF format, chain RA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain CB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain KA [auth B] MOL2 format, chain LB [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth F] MOL2 format, chain PA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth D]	AA [auth A] AB [auth D] BA [auth A] BB [auth D] CA [auth A] AA [auth A], AB [auth D], BA [auth A], BB [auth D], CA [auth A], CB [auth E], DA [auth A], DB [auth E], EA [auth A], EB [auth E], FA [auth A], FB [auth E], GA [auth B], GB [auth E], HA [auth B], HB [auth E], IA [auth B], IB [auth F], JA [auth B], JB [auth F], KA [auth B], KB [auth F], LA [auth B], LB [auth F], MA [auth B], MB [auth F], NA [auth B], NB [auth F], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth D], XA [auth D], Y [auth A], YA [auth D], Z [auth A], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain DA [auth A] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth B] Focus chain GB [auth E] Focus chain HA [auth B] Focus chain HB [auth E] Focus chain IA [auth B] Focus chain IB [auth F] Focus chain JA [auth B] Focus chain JB [auth F] Focus chain KA [auth B] Focus chain KB [auth F] Focus chain LA [auth B] Focus chain LB [auth F] Focus chain MA [auth B] Focus chain MB [auth F] Focus chain NA [auth B] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain DA [auth A] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth B] Focus chain GB [auth E] Focus chain HA [auth B] Focus chain HB [auth E] Focus chain IA [auth B] Focus chain IB [auth F] Focus chain JA [auth B] Focus chain JB [auth F] Focus chain KA [auth B] Focus chain KB [auth F] Focus chain LA [auth B] Focus chain LB [auth F] Focus chain MA [auth B] Focus chain MB [auth F] Focus chain NA [auth B] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D]