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- PDB-3qby: Crystal structure of the PWWP domain of human Hepatoma-derived gr... -

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Basic information

Entry
Database: PDB / ID: 3qby
TitleCrystal structure of the PWWP domain of human Hepatoma-derived growth factor 2
Components
  • H4K20me3 Histone H4 Peptide
  • Hepatoma-derived growth factor-related protein 2
KeywordsPROTEIN BINDING / hdgf2 / structural genomics consortium / SGC
Function / homology
Function and homology information


histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin ...histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / 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 / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA repair / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / 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 / TATA box binding protein associated factor ...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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / SH3 type barrels. / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H4 / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsZeng, H. / Tempel, W. / Amaya, M.F. / Adams-Cioaba, M.A. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Zeng, H. / Tempel, W. / Amaya, M.F. / Adams-Cioaba, M.A. / 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 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Sep 5, 2012Group: Derived calculations
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 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
B: Hepatoma-derived growth factor-related protein 2
C: Hepatoma-derived growth factor-related protein 2
H: H4K20me3 Histone H4 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,77626
Polymers33,5834
Non-polymers19222
Water93752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-35 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.527, 41.681, 156.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 3 / Fragment: UNP residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFRP2, HDGF2, UNQ785/PRO1604 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE / References: UniProt: Q7Z4V5
#2: Protein/peptide H4K20me3 Histone H4 Peptide


Mass: 1440.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P62805*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 20 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 2.5 M ammonium sulfate, 0.1 M sodium acetate, peptide ligand was added at 0.005 M concentration, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.94→25 Å / Num. obs: 21026 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.039 / Χ2: 1.738 / Net I/σ(I): 23.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-1.975.40.18210391.088198.3
1.97-2.015.80.1519981.1091100
2.01-2.055.90.12910351.1451100
2.05-2.095.70.10910551.2361100
2.09-2.146.10.0949971.2361100
2.14-2.185.90.08910431.3071100
2.18-2.246.10.08310161.288199.9
2.24-2.36.10.07510451.3881100
2.3-2.376.20.06810301.5021100
2.37-2.446.20.06410701.4771100
2.44-2.536.50.06110191.661100
2.53-2.636.50.05610421.6811100
2.63-2.756.80.0510541.7981100
2.75-2.96.90.04610421.8571100
2.9-3.0870.04210462.1261100
3.08-3.3270.03810652.1631100
3.32-3.6570.03510722.3781100
3.65-4.176.80.03310952.4421100
4.17-5.256.80.03210962.3651100
5.25-256.10.03111672.591199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EAE

3eae


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.598 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1055 5.131 %THIN SHELLS (sftools)
Rwork0.2164 ---
obs0.218 20561 99.651 %-
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: 73.98 Å2 / Biso mean: 33.681 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--0.167 Å20 Å2
3----1.237 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 30 52 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222140
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9492910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31923.53599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.489155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221713
X-RAY DIFFRACTIONr_mcbond_it0.6111.51286
X-RAY DIFFRACTIONr_mcangle_it1.04822057
X-RAY DIFFRACTIONr_scbond_it1.6583854
X-RAY DIFFRACTIONr_scangle_it2.5474.5851
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 (%)
1.95-200.2411480148699.596
2-2.0540.2491200.2191299142799.439
2.054-2.11300.1961419142999.3
2.113-2.1780.2411230.2071252138299.493
2.178-2.2480.269790.2151213129999.461
2.248-2.3260.213470.2111259131299.543
2.326-2.4130.2681110.2121111122999.43
2.413-2.50900.2251193119999.5
2.509-2.6190.2791000.2441069117199.829
2.619-2.7450.267780.2341034111599.731
2.745-2.890.257660.235979104799.809
2.89-3.06100.2261017101999.804
3.061-3.2670.29530.23588994599.683
3.267-3.5210.24580.226842900100
3.521-3.8460.273470.198782829100
3.846-4.280.208370.183719756100
4.28-4.9050.189620.168626688100
4.905-5.9180.223240.217576600100
5.918-8.0260.348310.242435466100
8.026-200.361190.28431233499.102
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8772-0.34280.48692.7555-0.96624.4072-0.08040.0391-0.2467-0.01970.14140.07580.1556-0.1178-0.0610.0109-0.01940.01160.0903-0.00030.09314.3323-16.2143-1.8222
23.3634-0.6698-1.41675.71160.60014.89490.139-0.12970.0532-0.2282-0.0094-0.24240.01490.1502-0.12960.2648-0.03080.0970.0636-0.0090.081518.558-13.24-32.6343
36.43753.5528-2.8456.3775-3.82258.047-0.19940.27530.1864-0.67670.31850.03640.484-0.0654-0.11910.1916-0.0490.00910.15340.01980.1731-1.6451-34.1639-19.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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