9GXE | pdb_00009gxe

Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule

PDB DOI: https://doi.org/10.2210/pdb9GXE/pdb
EM Map EMD-51659: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-09-30 Released: 2025-03-26
Deposition Author(s): Drulyte, I., Pellegrino, S., Harman, M., Bezerra, G.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9GXE

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

Literature

Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule

Drulyte, I., Pellegrino, S., Harman, M., Bezerra, G.A.

To be published.

Macromolecule Content

Total Structure Weight: 391.08 kDa
Atom Count: 26,514
Modeled Residue Count: 3,300
Deposited Residue Count: 3,447
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,133	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Homotrimeric bicycle molecule	D, E, F	16	synthetic construct	Mutation(s): 0

Oligosaccharides

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	G [auth AA], H [auth AB], I [auth AC], J [auth BA], K [auth BB], G [auth AA], H [auth AB], I [auth AC], J [auth BA], K [auth BB], L [auth BC], M [auth CA], N [auth CB], O [auth CC]	2		N-Glycosylation	Interactions Focus chain G [auth AA] Focus chain H [auth AB] Focus chain I [auth AC] Focus chain J [auth BA] Focus chain K [auth BB] Focus chain L [auth BC] Focus chain M [auth CA] Focus chain N [auth CB] Focus chain O [auth CC] Interactions & Density Focus chain G [auth AA] Focus chain H [auth AB] Focus chain I [auth AC] Focus chain J [auth BA] Focus chain K [auth BB] Focus chain L [auth BC] Focus chain M [auth CA] Focus chain N [auth CB] Focus chain O [auth CC]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain MA [auth C] SDF format, chain W [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain W [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain W [auth A]	FA [auth B], MA [auth C], W [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain MA [auth C] Focus chain W [auth A] Interactions & Density Focus chain FA [auth B] Focus chain MA [auth C] Focus chain W [auth A]
KZ0 (Subject of Investigation/LOI) Query on KZ0 Download:Ideal Coordinates CCD File SDF format, chain NA [auth D] SDF format, chain OA [auth E] SDF format, chain PA [auth F] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth F] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth F]	NA [auth D], OA [auth E], PA [auth F]	2,4,6-tris(chloromethyl)-1,3,5-triazine C₆ H₆ Cl₃ N₃ RICRAVHJCLFPFF-UHFFFAOYSA-N		Interactions Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F] Interactions & Density Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] 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 P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] 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 P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth B], Y [auth B], Z [auth B]	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 CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4J5 Query on 4J5	D, E, F	L-PEPTIDE LINKING	C₅ H₁₃ N₄ O₂		ARG
DAL Query on DAL	D, E, F	D-PEPTIDE LINKING	C₃ H₇ N O₂		--

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.