7BBH

Structure of Coronavirus Spike from Smuggled Guangdong Pangolin

PDB DOI: https://doi.org/10.2210/pdb7BBH/pdb
EM Map EMD-12130: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pangolin coronavirus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-12-17 Released: 2020-12-30
Deposition Author(s): Wrobel, A.G., Benton, D.J., Rosenthal, P.B., Gamblin, S.J.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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 and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2.

Wrobel, A.G., Benton, D.J., Xu, P., Calder, L.J., Borg, A., Roustan, C., Martin, S.R., Rosenthal, P.B., Skehel, J.J., Gamblin, S.J.

(2021) Nat Commun 12: 837-837

PubMed: 33547281 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-21006-9
Primary Citation of Related Structures:
7BBH

PubMed Abstract:
Coronaviruses of bats and pangolins have been implicated in the origin and evolution of the pandemic SARS-CoV-2. We show that spikes from Guangdong Pangolin-CoVs, closely related to SARS-CoV-2, bind strongly to human and pangolin ACE2 receptors. We also report the cryo-EM structure of a Pangolin-CoV spike protein and show it adopts a fully-closed conformation and that, aside from the Receptor-Binding Domain, it resembles the spike of a bat coronavirus RaTG13 more than that of SARS-CoV-2.

Organizational Affiliation

Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK. antoni.wrobel@crick.ac.uk.

Macromolecule Content

Total Structure Weight: 430.27 kDa
Atom Count: 25,827
Modelled Residue Count: 3,189
Deposited Residue Count: 3,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface glycoprotein	A, B, C	1,248	Pangolin coronavirus	Mutation(s): 3
UniProt
Find proteins for A0A6M3G9R1 (Pangolin coronavirus) Explore A0A6M3G9R1 Go to UniProtKB: A0A6M3G9R1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6M3G9R1
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.14

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-30

Deposition Author(s):

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001078
The Francis Crick Institute	United Kingdom	FC001143

Revision History (Full details and data files)

Version 1.0: 2020-12-30
Type: Initial release
Version 1.1: 2021-02-24
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary