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- PDB-3qj6: The crystal structure of PWWP domain of human Hepatoma-derived gr... -

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Basic information

Entry
Database: PDB / ID: 3qj6
TitleThe crystal structure of PWWP domain of human Hepatoma-derived growth factor 2 in complex with H3K79me3 peptide
Components
  • H3K79me3
  • Hepatoma-derived growth factor-related protein 2
KeywordsPROTEIN BINDING/ NUCLEAR PROTEIN / structural genomics consortium / histone / SGC / PROTEIN BINDING PROTEIN / PROTEIN BINDING- NUCLEAR PROTEIN complex
Function / homology
Function and homology information


H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / Chromatin modifying enzymes / telomere organization / methylated histone binding ...H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / Chromatin modifying enzymes / telomere organization / methylated histone binding / 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 / histone reader activity / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / 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 / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / DNA repair / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Histone H3 signature 1. ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / SH3 type barrels. - #140 / 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 / SH3 type barrels. / Core histone H2A/H2B/H3/H4 / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZeng, H. / Amaya, M.F. / Tempel, W. / Walker, J.R. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...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)
CitationJournal: Plos One / Year: 2011
Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 2
T: H3K79me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3535
Polymers12,2572
Non-polymers963
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-16 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.934, 74.934, 41.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 10714.236 Da / Num. of mol.: 1 / Fragment: UNP Q7Z4V5 residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFRP2, HDGF2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE / References: UniProt: Q7Z4V5
#2: Protein/peptide H3K79me3


Mass: 1542.732 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic peptide. Sequence occurs naturally in human, UNP P68431 residues 74-84
Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2.0M ammonium sulfate, 5% isopropanol. Protein was pre-incubated with 5 equivalents of peptide ligand, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 6094 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.085 / Χ2: 1.953 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3410.40.4663130.931100
2.34-2.3811.20.4422910.9211100
2.38-2.43110.3992920.9541100
2.43-2.4811.20.3633101.0181100
2.48-2.5311.10.3412990.9911100
2.53-2.5911.10.2783041.1411100
2.59-2.6611.10.2482991.0641100
2.66-2.7311.10.2122981.1541100
2.73-2.8111.10.1543031.2621100
2.81-2.911.10.1583031.2841100
2.9-3110.1213081.4381100
3-3.1211.10.1083011.4941100
3.12-3.26110.1053071.9551100
3.26-3.44110.0833052.1971100
3.44-3.6510.90.0742942.4791100
3.65-3.9310.70.0713122.9111100
3.93-4.3310.60.0633093.0581100
4.33-4.9510.50.0533012.6041100
4.95-6.2410.20.0483192.0851100
6.24-409.90.0533268.47199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3eae

3eae


Resolution: 2.3→37.468 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.307 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The program COOT and the MOLPROBITY server were also used.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 281 4.635 %RANDOM
Rwork0.2337 ---
obs0.236 6063 99.802 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 37.022 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.707 Å20.853 Å20 Å2
2--1.707 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms764 0 7 10 781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022799
X-RAY DIFFRACTIONr_bond_other_d0.0010.02562
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9561085
X-RAY DIFFRACTIONr_angle_other_deg0.79231359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.758592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77823.84639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07215107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.903152
X-RAY DIFFRACTIONr_chiral_restr0.070.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02172
X-RAY DIFFRACTIONr_mcbond_it0.4191.5477
X-RAY DIFFRACTIONr_mcbond_other0.0691.5186
X-RAY DIFFRACTIONr_mcangle_it0.7832759
X-RAY DIFFRACTIONr_scbond_it1.0793322
X-RAY DIFFRACTIONr_scangle_it1.7084.5326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.403170.303431448100
2.36-2.4240.31250.30340643399.538
2.424-2.4940.273200.27540042199.762
2.494-2.570.299190.2838140199.751
2.57-2.6540.366170.25838340199.751
2.654-2.7470.334170.245363380100
2.747-2.850.202210.21535137399.732
2.85-2.9660.24160.22334436299.448
2.966-3.0970.283100.266321331100
3.097-3.2470.335180.25931733799.407
3.247-3.4210.276170.232301318100
3.421-3.6260.299180.218265283100
3.626-3.8740.201140.197272286100
3.874-4.1810.366100.196253263100
4.181-4.5740.16100.184230240100
4.574-5.1050.31150.20721021699.537
5.105-5.8760.22490.219188197100
5.876-7.1530.22260.22116216999.408
7.153-9.9360.44960.247126132100
9.936-37.4680.27960.3957884100
Refinement TLS params.Method: refined / Origin x: 15.7272 Å / Origin y: 27.0252 Å / Origin z: -2.2485 Å
111213212223313233
T0.1192 Å20.0174 Å2-0.0222 Å2-0.0795 Å20.0084 Å2--0.0348 Å2
L7.5036 °2-0.2995 °2-4.7029 °2-4.8571 °20.3797 °2--11.9317 °2
S-0.121 Å °0.3632 Å °0.0812 Å °-0.3103 Å °0.0862 Å °-0.0888 Å °0.2888 Å °-0.4064 Å °0.0348 Å °

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