8Y4A

BA.2.86 S-trimer in complex with Nab XG2v046

PDB DOI: https://doi.org/10.2210/pdb8Y4A/pdb
EM Map EMD-38914: 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: 2024-01-30 Released: 2024-09-11
Deposition Author(s): Zhu, Q., Liu, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.

Zhu, Q., Liu, P., Liu, S., Yue, C., Wang, X.

(2024) Signal Transduct Target Ther 9: 217-217

PubMed: 39191733 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41392-024-01940-y
Primary Citation of Related Structures:
8Y4A, 8Y4C

Organizational Affiliation

CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 466.33 kDa
Atom Count: 29,416
Modelled Residue Count: 3,649
Deposited Residue Count: 4,072
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 C], C [auth A]	1,204	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 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: 18	Glycosylation Focus chain A [auth B] Focus chain B [auth C] Focus chain C [auth A]	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
XG2v046 Heavy chain	D [auth H], F [auth D]	122	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
XG2v046 Light chain	E [auth L], G [auth E]	108	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], I [auth G], J [auth I], M, N, H [auth F], I [auth G], J [auth I], M, N, O, R, S, T	2		N-Glycosylation	Interactions Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain M Focus chain N Focus chain O Focus chain R Focus chain S Focus chain T Interactions & Density Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain M Focus chain N Focus chain O Focus chain R Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J], P, Q, U	2		N-Glycosylation	Interactions Focus chain K [auth J] Focus chain P Focus chain Q Focus chain U Interactions & Density Focus chain K [auth J] Focus chain P Focus chain Q Focus chain U
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(8-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K]	3	N/A	N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]

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 B] SDF format, chain BA [auth B] SDF format, chain BB [auth A] SDF format, chain EB [auth A] SDF format, chain GB [auth A] SDF format, chain JA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain VA [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth A] SDF format, chain Z [auth B] SDF format, chain AB [auth A] SDF format, chain CA [auth B] SDF format, chain CB [auth A] SDF format, chain DA [auth B] SDF format, chain DB [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain HB [auth A] SDF format, chain IA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain UA [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain VA [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain AB [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain UA [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain VA [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain AB [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain UA [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain ZA [auth A]	AA [auth B] AB [auth A] BA [auth B] BB [auth A] CA [auth B] AA [auth B], AB [auth A], BA [auth B], BB [auth A], CA [auth B], CB [auth A], DA [auth B], DB [auth A], EA [auth B], EB [auth A], FA [auth B], FB [auth A], GA [auth B], GB [auth A], HA [auth B], HB [auth A], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth A], V [auth B], VA [auth A], W [auth B], WA [auth A], X [auth B], XA [auth A], Y [auth B], YA [auth A], Z [auth B], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth A] Focus chain BA [auth B] Focus chain BB [auth A] Focus chain CA [auth B] Focus chain CB [auth A] Focus chain DA [auth B] Focus chain DB [auth A] Focus chain EA [auth B] Focus chain EB [auth A] Focus chain FA [auth B] Focus chain FB [auth A] Focus chain GA [auth B] Focus chain GB [auth A] Focus chain HA [auth B] Focus chain HB [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth A] Focus chain V [auth B] Focus chain VA [auth A] Focus chain W [auth B] Focus chain WA [auth A] Focus chain X [auth B] Focus chain XA [auth A] Focus chain Y [auth B] Focus chain YA [auth A] Focus chain Z [auth B] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth A] Focus chain BA [auth B] Focus chain BB [auth A] Focus chain CA [auth B] Focus chain CB [auth A] Focus chain DA [auth B] Focus chain DB [auth A] Focus chain EA [auth B] Focus chain EB [auth A] Focus chain FA [auth B] Focus chain FB [auth A] Focus chain GA [auth B] Focus chain GB [auth A] Focus chain HA [auth B] Focus chain HB [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth A] Focus chain V [auth B] Focus chain VA [auth A] Focus chain W [auth B] Focus chain WA [auth A] Focus chain X [auth B] Focus chain XA [auth A] Focus chain Y [auth B] Focus chain YA [auth A] Focus chain Z [auth B] Focus chain ZA [auth A]