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- PDB-5b73: Crystal structure of human ZMYND8 PHD-Bromo-PWWP domain -

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Basic information

Entry
Database: PDB / ID: 5b73
TitleCrystal structure of human ZMYND8 PHD-Bromo-PWWP domain
ComponentsProtein kinase C-binding protein 1
KeywordsMETAL BINDING PROTEIN / zinc finger protein
Function / homology
Function and homology information


regulation of postsynaptic density protein 95 clustering / positive regulation of filopodium assembly / positive regulation of dendritic spine development / modulation of excitatory postsynaptic potential / site of DNA damage / positive regulation of dendritic spine maintenance / protein localization to chromatin / methylated histone binding / negative regulation of cell migration / dendritic shaft ...regulation of postsynaptic density protein 95 clustering / positive regulation of filopodium assembly / positive regulation of dendritic spine development / modulation of excitatory postsynaptic potential / site of DNA damage / positive regulation of dendritic spine maintenance / protein localization to chromatin / methylated histone binding / negative regulation of cell migration / dendritic shaft / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / lysine-acetylated histone binding / transcription corepressor activity / chromatin organization / nervous system development / DNA-binding transcription factor binding / dendritic spine / protein domain specific binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Protein kinase C-binding protein 1 / RACK7, Bromo domain / Protein kinase C-binding protein 1 / PRKCBP1, PHD finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. ...Protein kinase C-binding protein 1 / RACK7, Bromo domain / Protein kinase C-binding protein 1 / PRKCBP1, PHD finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
MYND-type zinc finger-containing chromatin reader ZMYND8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsLi, H. / Li, Y. / Zheng, X.
CitationJournal: Mol.Cell / Year: 2016
Title: ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes
Authors: Li, N. / Li, Y. / Lv, J. / Zheng, X. / Wen, H. / Shen, H. / Zhu, G. / Chen, T.Y. / Dhar, S.S. / Kan, P.Y. / Wang, Z. / Shiekhattar, R. / Shi, X. / Lan, F. / Chen, K. / Li, W. / Li, H. / Lee, M.G.
History
DepositionJun 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2604
Polymers39,0641
Non-polymers1963
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18220 Å2
Unit cell
Length a, b, c (Å)67.083, 67.999, 70.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein kinase C-binding protein 1


Mass: 39064.070 Da / Num. of mol.: 1 / Fragment: PHD-Bromo-PWWP domain, UNP residues 73-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULU4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→39.5 Å / Num. obs: 30158 / % possible obs: 99.3 % / Redundancy: 4.7 % / Net I/σ(I): 22.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
Cootmodel building
PHASERphasing
RefinementResolution: 1.8→39.5 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4
RfactorNum. reflection% reflection
Rfree0.2243 1344 4.46 %
Rwork0.1868 --
obs0.1886 30143 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 3 179 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122606
X-RAY DIFFRACTIONf_angle_d1.2583530
X-RAY DIFFRACTIONf_dihedral_angle_d13.458976
X-RAY DIFFRACTIONf_chiral_restr0.05370
X-RAY DIFFRACTIONf_plane_restr0.006455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8015-1.86590.2974920.22042808X-RAY DIFFRACTION98
1.8659-1.94060.3096690.2272917X-RAY DIFFRACTION100
1.9406-2.02890.26541180.21452870X-RAY DIFFRACTION100
2.0289-2.13580.2711270.20932869X-RAY DIFFRACTION100
2.1358-2.26970.23111890.19762833X-RAY DIFFRACTION100
2.2697-2.44490.25171380.19412862X-RAY DIFFRACTION100
2.4449-2.69090.25281440.19192877X-RAY DIFFRACTION99
2.6909-3.08010.22951750.19472863X-RAY DIFFRACTION100
3.0801-3.88010.20281340.17582930X-RAY DIFFRACTION99
3.8801-39.5140.20221580.17192970X-RAY DIFFRACTION97

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