9GWJ | pdb_00009gwj

Crystal structure of CINP-c1orf109 complex

PDB DOI: https://doi.org/10.2210/pdb9GWJ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-26 Released: 2025-10-08
Deposition Author(s): Masternak, M., Weisser, M., Montoya, G.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.69 Å
R-Value Free:
0.298 (Depositor), 0.298 (DCC)
R-Value Work:
0.265 (Depositor), 0.265 (DCC)
R-Value Observed:
0.267 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of CINP-c1orf109 complex

Masternak, M., Weisser, M., Montoya, G.

To be published.

Macromolecule Content

Total Structure Weight: 92.55 kDa
Atom Count: 6,460
Modeled Residue Count: 796
Deposited Residue Count: 796
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AFG2-interacting ribosome maturation factor	A, C	202	Homo sapiens	Mutation(s): 0 Gene Names: AIRIM, C1orf109
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX04 (Homo sapiens) Explore Q9NX04 Go to UniProtKB: Q9NX04
PHAROS: Q9NX04 GTEx: ENSG00000116922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NX04
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2-interacting protein	B, D	196	Homo sapiens	Mutation(s): 0 Gene Names: CINP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW66 (Homo sapiens) Explore Q9BW66 Go to UniProtKB: Q9BW66
PHAROS: Q9BW66 GTEx: ENSG00000100865
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BW66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.69 Å
R-Value Free: 0.298 (Depositor), 0.298 (DCC)
R-Value Work: 0.265 (Depositor), 0.265 (DCC)
R-Value Observed: 0.267 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.874	α = 90
b = 115.166	β = 90
c = 148.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF14CC0001

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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.