9B9L

RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide

PDB DOI: https://doi.org/10.2210/pdb9B9L/pdb

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

Deposited: 2024-04-02 Released: 2024-08-07
Deposition Author(s): Moreno, R.Y., Zhang, Y.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.347
R-Value Work: 0.266
R-Value Observed: 0.274

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Thr4 phosphorylation primes Ser2 phosphorylation on RNA polymerase II and mediates regulation in elongation and 3'end processing

Moreno, R.Y., Panina, S.B., Irani, S., Hardtke, H.A., Richardson, R., Floyd, B.M., Marcotte, E.M., Zhang, Q., Zhang, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 32.09 kDa
Atom Count: 2,172
Modelled Residue Count: 262
Deposited Residue Count: 277
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulation of nuclear pre-mRNA domain-containing protein 1B	A, B	131	Homo sapiens	Mutation(s): 0 Gene Names: RPRD1B, C20orf77, CREPT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQG5 (Homo sapiens) Explore Q9NQG5 Go to UniProtKB: Q9NQG5
PHAROS: Q9NQG5 GTEx: ENSG00000101413
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NQG5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER	C	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens) Explore P24928 Go to UniProtKB: P24928
PHAROS: P24928
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24928
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	C	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.347
R-Value Work: 0.266
R-Value Observed: 0.274
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.317	α = 90
b = 90.231	β = 90
c = 135.074	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-104896

Revision History (Full details and data files)

Version 1.0: 2024-08-07
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 R01GM133198.