8K5H

Structure of the SARS-CoV-2 BA.1 spike with UT28-RD

PDB DOI: https://doi.org/10.2210/pdb8K5H/pdb
EM Map EMD-36906: EMDB EMDataResource

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

Deposited: 2023-07-21 Released: 2023-12-27
Deposition Author(s): Chen, L., Kita, S., Anraku, Y., Maenaka, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

In silico-designed UT28K with two amino acid substitutions is capable of neutralization of resistant SARS-CoV2 Omicrons BA.1 valiant.

Ozawa, T., Ikeda, Y., Chen, L., Suzuki, R., Hoshino, A., Noguchi, A., Kita, S., Anraku, Y., Igarashi, E., Saga, Y., Inasaki, N., Taminishi, S., Sasaki, J., Kirita, Y., Fukuhara, H., Maenaka, K., Hashiguchi, T., Fukuhara, T., Hirabayashi, K., Tani, H., Kishi, H., Niimi, H.

To be published.

Macromolecule Content

Total Structure Weight: 463.44 kDa
Atom Count: 25,502
Modelled Residue Count: 3,171
Deposited Residue Count: 4,087
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth A], C	1,200	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 38 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UT28K-RD Fab heavy chain	D [auth H]	252	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UT28K-RD Fab light chain	E [auth L]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Interactions & Density Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain N [auth B] SDF format, chain NA [auth C] SDF format, chain O [auth B] SDF format, chain OA [auth C] SDF format, chain P [auth B] SDF format, chain PA [auth C] SDF format, chain Q [auth B] SDF format, chain QA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain UA [auth C] 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 A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth C] 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 A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth C], MA [auth C], N [auth B], NA [auth C], O [auth B], OA [auth C], P [auth B], PA [auth C], Q [auth B], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], TA [auth C], U [auth B], UA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] 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 C] Focus chain MA [auth C] Focus chain N [auth B] Focus chain NA [auth C] Focus chain O [auth B] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] 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 C] Focus chain MA [auth C] Focus chain N [auth B] Focus chain NA [auth C] Focus chain O [auth B] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101077 and JP22ama121010
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ae0121018
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K07624 and JP23H02776
Japan Agency for Medical Research and Development (AMED)	Japan	JP23fa627009
Other government		JPMJCR20H8