9B4X | pdb_00009b4x

SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA)

PDB DOI: https://doi.org/10.2210/pdb9B4X/pdb
EM Map EMD-44189: EMDB EMDataResource

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

Deposited: 2024-03-21 Released: 2025-04-16
Deposition Author(s): Singh, S., Hasan, S.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of SARS CoV-2 full-length spike with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation

Singh, S., Hasan, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 456.58 kDa
Atom Count: 26,191
Modeled Residue Count: 3,159
Deposited Residue Count: 3,936
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,312	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 8 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: 17	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], D, E, EA [auth e], AA [auth a], BA [auth b], D, E, EA [auth e], F, H, J, L, Q, S, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain D Focus chain E Focus chain EA [auth e] Focus chain F Focus chain H Focus chain J Focus chain L Focus chain Q Focus chain S Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain D Focus chain E Focus chain EA [auth e] Focus chain F Focus chain H Focus chain J Focus chain L Focus chain Q Focus chain S Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	CA [auth c], DA [auth d], FA [auth f], G, GA [auth g], CA [auth c], DA [auth d], FA [auth f], G, GA [auth g], I, IA [auth i], K, M, N, P, R, T, V, X, Y	3		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain I Focus chain IA [auth i] Focus chain K Focus chain M Focus chain N Focus chain P Focus chain R Focus chain T Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain I Focus chain IA [auth i] Focus chain K Focus chain M Focus chain N Focus chain P Focus chain R Focus chain T Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	O	6		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	U	4		N-Glycosylation	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], W	3		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain W Interactions & Density Focus chain HA [auth h] Focus chain W
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	JA [auth j]	5		N-Glycosylation	Interactions Focus chain JA [auth j] Interactions & Density Focus chain JA [auth j]
Glycosylation Resources
GlyTouCan: G10133VD GlyCosmos: G10133VD GlyGen: G10133VD

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 C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth B] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] KA [auth A] LA [auth A] MA [auth A] AB [auth C], BB [auth C], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]