9UAA | pdb_00009uaa

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8

PDB DOI: https://doi.org/10.2210/pdb9UAA/pdb
Entry: 9UAA supersedes: 8XNH
EM Map EMD-63983: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Henipavirus nipahense, Macaca
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-03-31 Released: 2025-04-09
Deposition Author(s): Fan, P.F., Ren, Y., Yu, C.M., Chen, W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.22 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

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6

Fan, P.F., Yu, C.M., Chen, W., Ren, Y.

To be published.

Macromolecule Content

Total Structure Weight: 224.96 kDa
Atom Count: 15,994
Modelled Residue Count: 2,013
Deposited Residue Count: 2,034
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, F [auth B], G [auth C]	445	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IH63 (Nipah virus) Explore Q9IH63 Go to UniProtKB: Q9IH63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9IH63
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain F [auth B] Focus chain G [auth C]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5C8-VL	B [auth F], H [auth E], I [auth D]	106	Macaca	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
5C8-VH	C [auth G], D [auth H], E [auth I]	127	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	J [auth A] K [auth A] L [auth A] M [auth B] N [auth B] J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]