9JNJ | pdb_00009jnj

Crystal structure of Human Cnot9

PDB DOI: https://doi.org/10.2210/pdb9JNJ/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-23 Released: 2025-09-24
Deposition Author(s): Yang, K.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Human Cnot9

Yang, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 122.09 kDa
Atom Count: 8,958
Modeled Residue Count: 1,065
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CCR4-NOT transcription complex subunit 9	A, B, C, D	268	Homo sapiens	Mutation(s): 0 Gene Names: CNOT9, RCD1, RQCD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92600 (Homo sapiens) Explore Q92600 Go to UniProtKB: Q92600
PHAROS: Q92600 GTEx: ENSG00000144580
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92600
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.069	α = 118.02
b = 68.773	β = 94.29
c = 69.53	γ = 93.67

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.