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- PDB-6iit: Complex structure of the HRP3 PWWP domain with both a 16-bp TA-ri... -

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Basic information

Entry
Database: PDB / ID: 6iit
TitleComplex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me2-containing histone peptide
Components
  • 16-bp TA-rich DNA
  • H3K36me2-containing histone peptide
  • Hepatoma-derived growth factor-related protein 3
KeywordsDNA BINDING PROTEIN/DNA / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of microtubule depolymerization / microtubule polymerization / Chromatin modifying enzymes / tubulin binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex ...negative regulation of microtubule depolymerization / microtubule polymerization / Chromatin modifying enzymes / tubulin binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / growth factor activity / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / neuron projection development / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / microtubule binding / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone H3.1 / Hepatoma-derived growth factor-related protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, Z. / Tian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570729 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and a H3K36me2-containing histone peptide
Authors: Wang, Z. / Tian, W.
History
DepositionOct 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 3
B: Hepatoma-derived growth factor-related protein 3
C: 16-bp TA-rich DNA
D: 16-bp TA-rich DNA
E: H3K36me2-containing histone peptide
F: H3K36me2-containing histone peptide


Theoretical massNumber of molelcules
Total (without water)34,7636
Polymers34,7636
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.592, 33.592, 200.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Hepatoma-derived growth factor-related protein 3 / HRP-3 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 11578.261 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL3, HDGF2, HDGFRP3, CGI-142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3E1
#2: DNA chain 16-bp TA-rich DNA


Mass: 4894.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide H3K36me2-containing histone peptide


Mass: 909.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaCl, 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 14978 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 36.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 753 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IIP

6iip


Resolution: 2.1→33.35 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2642 753 5.05 %
Rwork0.191 --
obs0.1944 14911 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 410 0 52 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082226
X-RAY DIFFRACTIONf_angle_d1.0863078
X-RAY DIFFRACTIONf_dihedral_angle_d20.09872
X-RAY DIFFRACTIONf_chiral_restr0.049295
X-RAY DIFFRACTIONf_plane_restr0.006331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.088-2.24920.28581700.22022780X-RAY DIFFRACTION98
2.2492-2.47550.34611610.22942794X-RAY DIFFRACTION100
2.4755-2.83360.28131550.22312856X-RAY DIFFRACTION100
2.8336-3.56930.29291280.20362859X-RAY DIFFRACTION100
3.5693-33.35440.22611390.16482869X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.2119 Å / Origin y: 9.897 Å / Origin z: 33.2081 Å
111213212223313233
T0.2813 Å20.0598 Å2-0.017 Å2-0.232 Å20.0125 Å2--0.2441 Å2
L0.4253 °20.2318 °20.395 °2-1.2233 °21.051 °2--1.43 °2
S0.0244 Å °0.0566 Å °0.0098 Å °0.0993 Å °0.0429 Å °0.0161 Å °0.1222 Å °0.1166 Å °-0.0684 Å °
Refinement TLS groupSelection details: all

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