6IIS

Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide

PDB DOI: https://doi.org/10.2210/pdb6IIS/pdb
NAKB: 6IIS

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: 2.36 Å
R-Value Free: 0.263
R-Value Work: 0.186
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide

Wang, Z., Tian, W.

(2019) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 34.79 kDa
Atom Count: 2,132
Modelled Residue Count: 228
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y3E1
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K36me3 peptide	E, F	8	Homo sapiens	Mutation(s): 0 Gene Names: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB... H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431
Entity Groups
UniProt Group	P68431
Protein Feature View 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
Protein Feature View Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L Query on M3L	E, F	L-PEPTIDE LINKING	C₉ H₂₁ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.263
R-Value Work: 0.186
R-Value Observed: 0.190
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.473	α = 90
b = 33.473	β = 90
c = 198.774	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.