3QJ6

The crystal structure of PWWP domain of human Hepatoma-derived growth factor 2 in complex with H3K79me3 peptide

PDB DOI: https://doi.org/10.2210/pdb3QJ6/pdb

Classification: PROTEIN BINDING/ NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-01-28 Released: 2011-02-23
Deposition Author(s): Zeng, H., Amaya, M.F., Tempel, W., Walker, J.R., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.276
R-Value Work: 0.234
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural and Histone Binding Ability Characterizations of Human PWWP Domains.

Wu, H., Zeng, H., Lam, R., Tempel, W., Amaya, M.F., Xu, C., Dombrovski, L., Qiu, W., Wang, Y., Min, J.

(2011) PLoS One 6: e18919-e18919

PubMed: 21720545 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0018919
Primary Citation of Related Structures:
3EAE, 3L42, 3LLR, 3LYI, 3MO8, 3PFS, 3PMI, 3QBY, 3QJ6, 3QKJ

PubMed Abstract:
The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently.

Organizational Affiliation

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 12.35 kDa
Atom Count: 781
Modelled Residue Count: 95
Deposited Residue Count: 106
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 2	A	94	Homo sapiens	Mutation(s): 0 Gene Names: HDGFRP2, HDGF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4V5 (Homo sapiens) Explore Q7Z4V5 Go to UniProtKB: Q7Z4V5
GTEx: ENSG00000167674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z4V5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K79me3	B [auth T]	12	Homo sapiens	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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L Query on M3L	B [auth T]	L-PEPTIDE LINKING	C₉ H₂₁ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.276
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.934	α = 90
b = 74.934	β = 90
c = 41.764	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description