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- PDB-2rr4: Complex structure of the zf-CW domain and the H3K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 2rr4
TitleComplex structure of the zf-CW domain and the H3K4me3 peptide
Components
  • Histone H3
  • Zinc finger CW-type PWWP domain protein 1
KeywordsMetal-binding protein/nuclear Protein / zf-CW domain / ZCWPW1 / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Metal-binding protein-nuclear Protein complex
Function / homology
Function and homology information


histone H3K4me3 reader activity / positive regulation of DNA recombination / homologous chromosome pairing at meiosis / meiosis I / methyl-CpG binding / positive regulation of double-strand break repair / Chromatin modifying enzymes / : / telomere organization / Interleukin-7 signaling ...histone H3K4me3 reader activity / positive regulation of DNA recombination / homologous chromosome pairing at meiosis / meiosis I / methyl-CpG binding / positive regulation of double-strand break repair / Chromatin modifying enzymes / : / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / 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 / histone reader activity / 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 / 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 / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / 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) / Oxidative Stress Induced Senescence / gene expression / spermatogenesis / Estrogen-dependent gene expression / cell differentiation / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Zinc finger CW-type PWWP domain protein ZCWPW1/ZCWPW2 / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain ...Zinc finger CW-type PWWP domain protein ZCWPW1/ZCWPW2 / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3 / Histone H3.1 / Zinc finger CW-type PWWP domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsHe, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2010
Title: Structural insight into the zinc finger CW domain as a histone modification reader
Authors: He, F. / Umehara, T. / Saito, K. / Harada, T. / Watanabe, S. / Yabuki, T. / Kigawa, T. / Takahashi, M. / Kuwasako, K. / Tsuda, K. / Matsuda, T. / Aoki, M. / Seki, E. / Kobayashi, N. / ...Authors: He, F. / Umehara, T. / Saito, K. / Harada, T. / Watanabe, S. / Yabuki, T. / Kigawa, T. / Takahashi, M. / Kuwasako, K. / Tsuda, K. / Matsuda, T. / Aoki, M. / Seki, E. / Kobayashi, N. / Guntert, P. / Yokoyama, S. / Muto, Y.
History
DepositionMar 24, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger CW-type PWWP domain protein 1
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9063
Polymers8,8412
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1306.4 Å2
ΔGint-7 kcal/mol
Surface area6380.7 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger CW-type PWWP domain protein 1 / zf-CW


Mass: 7648.352 Da / Num. of mol.: 1 / Fragment: zf-CW domain, residues 246-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E. coli - cell free / Gene: ZCWPW1 / Plasmid: P060116-12 / Production host: cell free synthsis (unknown) / References: UniProt: Q9H0M4
#2: Protein/peptide Histone H3


Mass: 1192.412 Da / Num. of mol.: 1 / Fragment: Histone H3 tail, UNP residues 2-11 / Source method: obtained synthetically / Details: chemical synthesized, purchased / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K4Y7, UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 20mM D-tris-HCl(PH 7.0); 100mM NaCl; 0.02% D-DTT; 50micro-M ZNCl2+1mM IDA; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMentity_1-1[U-13C; U-15N]1
1.1 mMN-TRIMETHYLLYSINE-21
50 uMZINC ION-31
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
NMRView5Johnson, One Moon Scientificdata analysis
XwinNMR3Bruker Biospincollection
KUJIRA0.9839Naohiro Kobayashidata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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