9UYD | pdb_00009uyd

SARS-CoV-2 Ancestral strain spike S-cred

PDB DOI: https://doi.org/10.2210/pdb9UYD/pdb
EM Map EMD-64609: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-15 Released: 2026-06-10
Deposition Author(s): Hemmi, T., Yajima, H., Hashiguchi, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UYD

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

Literature

SARS-CoV-2 Ancestral strain spike S-cred

Hemmi, T., Yajima, H., Hashiguchi, T.

To be published.

Macromolecule Content

Total Structure Weight: 382 kDa
Atom Count: 22,743
Modeled Residue Count: 2,934
Deposited Residue Count: 3,360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C [auth F]	1,120	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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: 12	Glycosylation Focus chain A Focus chain B Focus chain C [auth F]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	D [auth L], E [auth M], F [auth N], G [auth C], H [auth D], D [auth L], E [auth M], F [auth N], G [auth C], H [auth D], I [auth E], J [auth G], K [auth H], L [auth I]	2		N-Glycosylation	Interactions Focus chain D [auth L] Focus chain E [auth M] Focus chain F [auth N] Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I] Interactions & Density Focus chain D [auth L] Focus chain E [auth M] Focus chain F [auth N] Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) 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 F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] 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 U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain T [auth A] SDF format, chain HA [auth F] 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 F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] 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 U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth A] MOL2 format, chain HA [auth F] 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 F] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] 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 U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth A] mmCIF format, chain HA [auth F]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth F] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth F], FA [auth F], GA [auth F], HA [auth F], IA [auth F], JA [auth F], KA [auth F], LA [auth F], M [auth A], MA [auth F], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], 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 F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] 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 B] Focus chain W [auth B] 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 F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] 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 B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23KJ1304

Revision History (Full details and data files)

Version 1.0: 2026-06-10
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.