9CIN | pdb_00009cin

Fab fragment of Antibody with NiV glycoprotein F

PDB DOI: https://doi.org/10.2210/pdb9CIN/pdb
EM Map EMD-45622: EMDB EMDataResource

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

Deposited: 2024-07-03 Released: 2026-01-28
Deposition Author(s): Ouizougun-Oubari, M., Bajic, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.03 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9CIN

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

Literature

Broadly neutralizing antibody in complex with Nipah fusion glycoprotein

Bajic, G., Ouizougun-Oubari, M.

To be published.

Macromolecule Content

Total Structure Weight: 261.94 kDa
Atom Count: 15,798
Modeled Residue Count: 2,007
Deposited Residue Count: 2,343
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, F [auth B], G [auth C]	552	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IH63 (Nipah virus) Explore Q9IH63 Go to UniProtKB: Q9IH63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9IH63
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain F [auth B] Focus chain G [auth C]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Heavy Chain	B [auth H], C [auth J], D [auth M]	122	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Light Chain	E [auth L], H [auth K], I [auth N]	107	Mus musculus	Mutation(s): 0

Oligosaccharides

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth E], M [auth G], O	4		N-Glycosylation	Interactions Focus chain K [auth E] Focus chain M [auth G] Focus chain O Interactions & Density Focus chain K [auth E] Focus chain M [auth G] Focus chain O
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.03 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Ouizougun-Oubari, M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-01-28
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.