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- PDB-4o62: CW-type zinc finger of ZCWPW2 in complex with the amino terminus ... -

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Basic information

Entry
Database: PDB / ID: 4o62
TitleCW-type zinc finger of ZCWPW2 in complex with the amino terminus of histone H3
Components
  • Histone H3.3
  • Zinc finger CW-type PWWP domain protein 2
KeywordsMETAL/DNA BINDING PROTEIN / zinc finger / histone / Structural Genomics / Structural Genomics Consortium / SGC / METAL-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / : / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / 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) / SIRT1 negatively regulates rRNA 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) / 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 / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / 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 / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / 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. / Herpes Virus-1 / PWWP domain / PWWP domain profile. / PWWP domain / Histone H3 signature 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. / Herpes Virus-1 / 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
H3.3 histone B / Histone H3.3 / Zinc finger CW-type PWWP domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsLiu, Y. / Tempel, W. / Dong, A. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins.
Authors: Liu, Y. / Tempel, W. / Zhang, Q. / Liang, X. / Loppnau, P. / Qin, S. / Min, J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
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_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Zinc finger CW-type PWWP domain protein 2
B: Zinc finger CW-type PWWP domain protein 2
C: Zinc finger CW-type PWWP domain protein 2
D: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72634
Polymers22,5304
Non-polymers19630
Water3,045169
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.095, 127.095, 63.046
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Zinc finger CW-type PWWP domain protein 2


Mass: 7078.734 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 21-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCWPW2 / Plasmid: pET28a-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-V2R-pRARE2 / References: UniProt: Q504Y3
#2: Protein/peptide Histone H3.3


Mass: 1293.516 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-12 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: K7ES00, UniProt: P84243*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 27 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.6 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 2 M ammonium sulfate, 2% PEG400, 0.1 M sodium HEPES, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28303 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28303 Å / Relative weight: 1
ReflectionResolution: 1.78→41.46 Å / Num. obs: 36371 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 1.5 / Num. measured all: 11373 / Num. unique all: 2051 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.78→41.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1777 / WRfactor Rwork: 0.1557 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8528 / SU B: 3.963 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0728 / SU Rfree: 0.0739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MODEL AUTO BUILDING WAS PERFORMED WIT ARP/WARP. MANUAL MODEL BUILDING WAS DONE IN COOT. MODEL GEOMETRY WAS VALIDATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1587 4.4 %THIN SHELLS (SFTOOLS)
Rwork0.1646 ---
obs0.1656 36369 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.64 Å2 / Biso mean: 36.6352 Å2 / Biso min: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0.5 Å20 Å2
2---1.01 Å20 Å2
3---3.27 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 30 169 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021518
X-RAY DIFFRACTIONr_bond_other_d0.0010.021300
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9092067
X-RAY DIFFRACTIONr_angle_other_deg0.74733002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33525.61889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1115254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.769157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_mcbond_it2.4892.204708
X-RAY DIFFRACTIONr_mcbond_other2.4482.193707
X-RAY DIFFRACTIONr_mcangle_it3.3343.254880
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 181 -
Rwork0.281 2487 -
all-2668 -
obs--100 %
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)
15.51713.9482-0.2815.01010.63021.50660.0757-0.25470.14830.0271-0.16860.30710.0283-0.37330.09290.0112-0.021-0.01990.1434-0.00560.07242.509825.586433.5332
22.4753-1.26570.63087.3716-2.11732.11920.0013-0.1092-0.11490.2519-0.0107-0.34060.24060.2180.00940.17040.0182-0.04540.0482-0.00280.169119.019610.462829.511
32.653.0707-1.94726.6815-2.63842.82720.0230.055-0.1315-0.1589-0.1088-0.09630.1567-0.07380.08580.03130.0022-0.01220.0147-0.00020.023917.860134.260119.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 1001
2X-RAY DIFFRACTION2B22 - 1001
3X-RAY DIFFRACTION3C21 - 1001

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