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- PDB-9t2g: Human PRKCBP1 zinc finger MYND-type containing 8 with crystalliza... -

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Basic information

Entry
Database: PDB / ID: 9t2g
TitleHuman PRKCBP1 zinc finger MYND-type containing 8 with crystallization epitope mutations N221R:M226H
ComponentsMYND-type zinc finger-containing chromatin reader ZMYND8
KeywordsTRANSFERASE / crystal epitope
Function / homology
Function and homology information


regulation of postsynaptic density protein 95 clustering / histone H3K14ac reader activity / histone H3K4me1 reader activity / 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 ...regulation of postsynaptic density protein 95 clustering / histone H3K14ac reader activity / histone H3K4me1 reader activity / 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 / negative regulation of cell migration / dendritic shaft / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / transcription corepressor activity / nervous system development / dendritic spine / DNA-binding transcription factor binding / 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 / ZMYND8 protein coiled-coil / PRKCBP1, PHD finger / : / ZMYND11/ZMYD8, MYND zinc finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type ...Protein kinase C-binding protein 1 / RACK7, Bromo domain / : / Protein kinase C-binding protein 1 / ZMYND8 protein coiled-coil / PRKCBP1, PHD finger / : / ZMYND11/ZMYD8, MYND zinc finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. ...Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionOct 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYND-type zinc finger-containing chromatin reader ZMYND8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0804
Polymers37,8841
Non-polymers1963
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.802, 71.929, 72.529
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MYND-type zinc finger-containing chromatin reader ZMYND8 / Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Protein ...Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Protein kinase C-binding protein 1 / Rack7 / Transcription coregulator ZMYND8 / Zinc finger MYND domain-containing protein 8


Mass: 37883.773 Da / Num. of mol.: 1 / Mutation: N221R:M226H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND8, KIAA1125, PRKCBP1, RACK7 / 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.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M lithium sulfate 25% PEG3350 0.1M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.66→72.53 Å / Num. obs: 42980 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.3
Reflection shellResolution: 1.66→1.7 Å / Rmerge(I) obs: 3.212 / Num. unique obs: 3108

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→49.92 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2163 -RANDOM
Rwork0.2372 ---
obs0.2388 42510 98.4 %-
Displacement parametersBiso mean: 25.58 Å2
Baniso -1Baniso -2Baniso -3
1-7.2686 Å20 Å20 Å2
2---0.5112 Å20 Å2
3----6.7574 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.66→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 3 348 2869
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969242HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1478SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes801HARMONIC5
X-RAY DIFFRACTIONt_it2599HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion329SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4001SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion15.34
LS refinement shellResolution: 1.66→1.67 Å
RfactorNum. reflection% reflection
Rfree0.3643 59 -
Rwork0.3699 --
obs0.3695 851 96.71 %

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