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- PDB-9t2f: Crystal structure of human PRKCBP1 Zinc finger MYND-type containi... -

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Basic information

Entry
Database: PDB / ID: 9t2f
TitleCrystal structure of human PRKCBP1 Zinc finger MYND-type containing 8 with pentaglutamate tag
ComponentsMYND-type zinc finger-containing chromatin reader ZMYND8
KeywordsTRANSCRIPTION / Substrate Complex / GDP-L-Fucose / L-Fucose
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: 1.68 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 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

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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)38,8415
Polymers38,5821
Non-polymers2584
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.04, 72.09, 68.67
Angle α, β, γ (deg.)90, 127.02, 90
Int Tables number5
Space group name H-MC121

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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: 38582.441 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350 0.2M sodium chloride 0.1M bis-tris pH 5.5

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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: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.68→54.83 Å / Num. obs: 47262 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 2841

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→54.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 2308 -RANDOM
Rwork0.2123 ---
obs0.2134 47262 98.5 %-
Displacement parametersBiso mean: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1--5.8846 Å20 Å2-8.8605 Å2
2--3.6244 Å20 Å2
3---2.2602 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.68→54.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 7 259 2767
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092590HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93514HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d881SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes433HARMONIC5
X-RAY DIFFRACTIONt_it2590HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1874SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.37
LS refinement shellResolution: 1.68→1.69 Å
RfactorNum. reflection% reflection
Rfree0.3522 44 -
Rwork0.3434 --
obs0.3439 946 98.66 %

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