6IIT | pdb_00006iit

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.264 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

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

Macromolecules

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 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 ID: 2
Molecule	Chains	Length	Organism	Image
16-bp TA-rich DNA	C, D	16	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Wang, Z., Tian, W.

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

Revision History  

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