9RDT | pdb_00009rdt

Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein

PDB DOI: https://doi.org/10.2210/pdb9RDT/pdb
EM Map EMD-53938: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Sarbecovirus sp. RhGB07
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2025-06-03 Released: 2025-09-24
Deposition Author(s): Lau, K., Dong, C.N., Ekundayo, B.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Understanding the future risk of bat coronavirus spillover into humans - correlating sarbecovirus receptor usage, host range, and antigenicity

Thakur, N., Newman, J., Ni, D., Seow, J., Hay, A.L., Li, Y., Upadhyay, A., Ekundayo, B.E., Peacock, T.P., Lau, K., Doores, K.J., Bailey, D.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.09.03.673949

Macromolecule Content

Total Structure Weight: 441.35 kDa
Atom Count: 27,117
Modeled Residue Count: 3,273
Deposited Residue Count: 3,765
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RhGB07 Spike- T4 foldon fusion protein	A [auth C], B, C [auth A]	1,255	Sarbecovirus sp. RhGB07	Mutation(s): 0

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, FA [auth f], R	2		N/A	Interactions Focus chain D Focus chain FA [auth f] Focus chain R Interactions & Density Focus chain D Focus chain FA [auth f] Focus chain R
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], E, EA [auth e], F, BA [auth b], CA [auth c], E, EA [auth e], F, GA [auth g], HA [auth h], J, K, LA [auth l], MA [auth m], N, O, PA [auth p], Q, QA [auth q], S, SA [auth s], T, X, Y	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain K Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain O Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain X Focus chain Y Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain K Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain O Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], G, H, I, IA [auth i], DA [auth d], G, H, I, IA [auth i], JA [auth j], KA [auth k], L, NA [auth n], P, RA [auth r], U, V, W, Z	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain G Focus chain H Focus chain I Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain L Focus chain NA [auth n] Focus chain P Focus chain RA [auth r] Focus chain U Focus chain V Focus chain W Focus chain Z Interactions & Density Focus chain DA [auth d] Focus chain G Focus chain H Focus chain I Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain L Focus chain NA [auth n] Focus chain P Focus chain RA [auth r] Focus chain U Focus chain V Focus chain W Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], M, OA [auth o]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain M Focus chain OA [auth o] Interactions & Density Focus chain AA [auth a] Focus chain M Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 ZA [auth B] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain KB [auth A] SDF format, chain JB [auth A] SDF format, chain IB [auth A] SDF format, chain HB [auth A] SDF format, chain GB [auth A] SDF format, chain FB [auth A] SDF format, chain EB [auth B] SDF format, chain DB [auth B] SDF format, chain CB [auth B] SDF format, chain BB [auth B] SDF format, chain AB [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain KB [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain AB [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain KB [auth A] mmCIF format, chain JB [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain AB [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth A], GB [auth A], HB [auth A], IB [auth A], JB [auth A], KB [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth A] Focus chain KB [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth A] Focus chain KB [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2+220824
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.