6IIT

Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me2-containing histone peptide

PDB DOI: https://doi.org/10.2210/pdb6IIT/pdb
NAKB: 6IIT

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-07 Released: 2019-04-24
Deposition Author(s): Wang, Z., Tian, W.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.264
R-Value Work: 0.191
R-Value Observed: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and a H3K36me2-containing histone peptide

Wang, Z., Tian, W.

(2019) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 34.76 kDa
Atom Count: 2,170
Modelled Residue Count: 229
Deposited Residue Count: 248
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 3	A, B	100	Homo sapiens	Mutation(s): 0 Gene Names: HDGFL3, HDGF2, HDGFRP3, CGI-142
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3E1 (Homo sapiens) Explore Q9Y3E1 Go to UniProtKB: Q9Y3E1
PHAROS: Q9Y3E1 GTEx: ENSG00000166503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y3E1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K36me2-containing histone peptide	E, F	8	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
16-bp TA-rich DNA	C, D	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	E, F	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.264
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.592	α = 90
b = 33.592	β = 90
c = 200.101	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570729

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.