9B8F | pdb_00009b8f

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

PDB DOI: https://doi.org/10.2210/pdb9B8F/pdb
EM Map EMD-44344: EMDB EMDataResource

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

Deposited: 2024-03-29 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: 4.15 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

Structure of SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 2RBD-up conformation

Singh, S., Hasan, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 455.46 kDa
Atom Count: 26,292
Modeled Residue Count: 3,193
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: 13	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], D, L, M, N, BA [auth b], D, L, M, N, P, R, S, U, V, W, X	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain D Focus chain L Focus chain M Focus chain N Focus chain P Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain D Focus chain L Focus chain M Focus chain N Focus chain P Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
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	E, F	4		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e], FA [auth f], G, I, K, EA [auth e], FA [auth f], G, I, K, O, Q, T	2		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain I Focus chain K Focus chain O Focus chain Q Focus chain T Interactions & Density Focus chain EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain I Focus chain K Focus chain O Focus chain Q Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	4		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	J, Z	4		N-Glycosylation	Interactions Focus chain J Focus chain Z Interactions & Density Focus chain J Focus chain Z
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
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	Y	3		N/A	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 8
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], DA [auth d]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
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-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c]	4		N-Glycosylation	Interactions Focus chain CA [auth c] Interactions & Density Focus chain CA [auth c]

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