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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


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 / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening ...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 / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / 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 / chromosome / 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) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell differentiation / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
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. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Herpes Virus-1 ...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. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Herpes Virus-1 / 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
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

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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: 7.0 / 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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