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- PDB-4z0r: Crystal Structure of the CW domain of ZCWPW2 mutant F78R in compl... -

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Basic information

Entry
Database: PDB / ID: 4z0r
TitleCrystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide
Components
  • Histone H3.1Histone H3
  • Zinc finger CW-type PWWP domain protein 2
KeywordsPROTEIN BINDING/STRUCTURAL PROTEIN / structural genomics / cw domain / Structural Genomics Consortium / SGC / PROTEIN BINDING-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


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 / HCMV Late Events ...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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / 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. / PWWP domain / PWWP domain profile. / PWWP domain / Herpes Virus-1 / 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. / 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 H3.1 / Zinc finger CW-type PWWP domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide
Authors: Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_entity_src_syn ...entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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 H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,22733
Polymers22,8724
Non-polymers35429
Water2,342130
1
A: Zinc finger CW-type PWWP domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,25014
Polymers7,0891
Non-polymers16113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area4590 Å2
MethodPISA
2
B: Zinc finger CW-type PWWP domain protein 2
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,82213
Polymers8,6952
Non-polymers12711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area4800 Å2
MethodPISA
3
C: Zinc finger CW-type PWWP domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1546
Polymers7,0891
Non-polymers655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area4430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.659, 126.659, 63.271
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Zinc finger CW-type PWWP domain protein 2 / zcwpw2


Mass: 7088.754 Da / Num. of mol.: 3 / Fragment: CW domain (UNP residues 21-78) / Mutation: F78R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCWPW2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q504Y3
#2: Protein/peptide Histone H3.1 / Histone H3 / Histone H3


Mass: 1605.885 Da / Num. of mol.: 1 / Fragment: N-terminal tail (UNP residues 2-16) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 5 types, 159 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Num. of mol.: 24 / Source method: obtained synthetically
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4.5 Å3/Da / Density % sol: 72.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.75→41.442 Å / Num. obs: 37974 / % possible obs: 99.4 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Net I/σ(I): 14.3 / Num. measured all: 209970
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.75-1.785.71.0391.51199021140.6650.481100
9.09-41.445.10.04937.913202600.9860.02594.3

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.2data scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementStarting model: PDB entry 4O62

4o62


Resolution: 1.75→41.442 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1942 / WRfactor Rwork: 0.1747 / FOM work R set: 0.8596 / SU B: 4.336 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 1580 4.2 %THIN SHELLS (SFTOOLS)
Rwork0.1771 36394 --
obs0.1777 -99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.48 Å2 / Biso mean: 33.923 Å2 / Biso min: 19.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0.28 Å20 Å2
2---0.56 Å20 Å2
3---1.8 Å2
Refinement stepCycle: final / Resolution: 1.75→41.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 36 130 1649
Biso mean--42.14 39 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021593
X-RAY DIFFRACTIONr_bond_other_d0.0020.021382
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9142174
X-RAY DIFFRACTIONr_angle_other_deg0.98233179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.30525.16591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6411510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021856
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
X-RAY DIFFRACTIONr_mcbond_it1.7931.963751
X-RAY DIFFRACTIONr_mcbond_other1.7891.959749
X-RAY DIFFRACTIONr_mcangle_it2.5682.92937
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 29 -
Rwork0.296 2813 -
all-2842 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: 13.8218 Å / Origin y: 22.4781 Å / Origin z: 27.6178 Å
111213212223313233
T0.0784 Å2-0.0326 Å2-0.0439 Å2-0.0261 Å20.0165 Å2--0.1328 Å2
L1.1169 °20.8594 °2-0.3282 °2-2.1047 °2-0.6396 °2--1.4507 °2
S0.0451 Å °-0.0866 Å °-0.0998 Å °-0.0535 Å °-0.1262 Å °-0.1344 Å °0.2598 Å °-0.1002 Å °0.0811 Å °

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