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

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Basic information

Entry
Database: PDB / ID: 6iis
TitleComplex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide
Components
  • 16-bp TA-rich DNA
  • H3K36me3 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 / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / tubulin binding / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation ...negative regulation of microtubule depolymerization / microtubule polymerization / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / tubulin binding / 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) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / growth factor activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / HCMV Early Events / neuron projection development / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / 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 / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / 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 / 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: 2.358 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 an H3K36me3-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

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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: H3K36me3 peptide
F: H3K36me3 peptide


Theoretical massNumber of molelcules
Total (without water)34,7936
Polymers34,7936
Non-polymers00
Water32418
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)33.473, 33.473, 198.774
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 H3K36me3 peptide


Mass: 924.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.85 Å3/Da / Density % sol: 33.44 %
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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 9478 / % possible obs: 91.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2 / Num. unique obs: 481

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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: 2.358→33.129 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 34.35
RfactorNum. reflection% reflection
Rfree0.2634 455 4.83 %
Rwork0.1859 --
obs0.1896 9426 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.358→33.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 410 0 18 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012222
X-RAY DIFFRACTIONf_angle_d1.3143076
X-RAY DIFFRACTIONf_dihedral_angle_d21.593868
X-RAY DIFFRACTIONf_chiral_restr0.057294
X-RAY DIFFRACTIONf_plane_restr0.007330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3576-2.69860.381610.25232969X-RAY DIFFRACTION91
2.6986-3.39940.28521310.21322987X-RAY DIFFRACTION90
3.3994-33.13230.23091630.16023015X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 51.0367 Å / Origin y: -17.8991 Å / Origin z: 230.9349 Å
111213212223313233
T0.3455 Å2-0.0379 Å2-0.0029 Å2-0.2638 Å2-0.0413 Å2--0.2938 Å2
L0.6079 °2-0.2484 °20.5575 °2-1.3026 °2-1.3826 °2--1.6019 °2
S0.0613 Å °-0.0717 Å °0.0114 Å °-0.1468 Å °0.0118 Å °-0.0585 Å °0.2601 Å °-0.1596 Å °-0.056 Å °
Refinement TLS groupSelection details: all

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