9JNM | pdb_00009jnm

Human MEX3B CBM 26-46aa peptide bound to human CNOT9

PDB DOI: https://doi.org/10.2210/pdb9JNM/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: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Human MEX3B CBM 26-46aa peptide bound to human CNOT9

Yang, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 33.17 kDa
Atom Count: 2,531
Modeled Residue Count: 290
Deposited Residue Count: 291
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CCR4-NOT transcription complex subunit 9	A	267	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein MEX3B	B	24	Homo sapiens	Mutation(s): 0 Gene Names: MEX3B, KIAA2009, RKHD3, RNF195
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZN04 (Homo sapiens) Explore Q6ZN04 Go to UniProtKB: Q6ZN04
PHAROS: Q6ZN04 GTEx: ENSG00000183496
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZN04
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.854	α = 90
b = 65.854	β = 90
c = 333.427	γ = 120

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.