8YKG | pdb_00008ykg

Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-up state)

PDB DOI: https://doi.org/10.2210/pdb8YKG/pdb
EM Map EMD-39370: EMDB EMDataResource

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

Deposited: 2024-03-05 Released: 2025-03-12
Deposition Author(s): Anraku, Y., Kita, S., Onodera, T., Tadokoro, T., Ito, S., Adachi, Y., Kotaki, R., Suzuki, T., Hashiguchi, T., Takahashi, Y., Maenaka, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 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

Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108

Anraku, Y., Maenaka, K.

To be published.

Macromolecule Content

Total Structure Weight: 456.96 kDa
Atom Count: 26,426
Modelled Residue Count: 3,353
Deposited Residue Count: 4,099
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,199	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NT-108 scFv	D, E [auth F]	251	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: 3
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 E], G	2		N-Glycosylation	Interactions Focus chain F [auth E] Focus chain G Interactions & Density Focus chain F [auth E] Focus chain G

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 H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth C]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP17am0101093
Japan Agency for Medical Research and Development (AMED)	Japan	JP20ae0101047
Japan Agency for Medical Research and Development (AMED)	Japan	JP21fk0108463
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121037
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H05873
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627005
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627009
Japan Agency for Medical Research and Development (AMED)	Japan	JP23jf0126002