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- PDB-5mq4: Crystal Structure of the leucine zipper of human PRKCBP1 -

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Basic information

Entry
Database: PDB / ID: 5mq4
TitleCrystal Structure of the leucine zipper of human PRKCBP1
ComponentsProtein kinase C-binding protein 1
KeywordsTRANSFERASE / Leucine zipper
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 / nervous system development / chromatin organization / 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 / SAD / Resolution: 2.7 Å
AuthorsKrojer, T. / Savitsky, P. / Picaud, S. / Newman, J. / Tallant, C. / Heroven, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Filippakopoulos, P.
CitationJournal: To Be Published
Title: Crystal Structure of the leucine zipper of human PRKCBP1
Authors: Krojer, T. / Savitsky, P. / Picaud, S. / Filippakopoulos, P.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C-binding protein 1
B: Protein kinase C-binding protein 1
C: Protein kinase C-binding protein 1
D: Protein kinase C-binding protein 1
E: Protein kinase C-binding protein 1
F: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,61423
Polymers90,3496
Non-polymers1,26517
Water181
1
A: Protein kinase C-binding protein 1
D: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5708
Polymers30,1162
Non-polymers4546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-68 kcal/mol
Surface area16440 Å2
MethodPISA
2
B: Protein kinase C-binding protein 1
F: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5708
Polymers30,1162
Non-polymers4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-65 kcal/mol
Surface area16540 Å2
MethodPISA
3
C: Protein kinase C-binding protein 1
E: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4747
Polymers30,1162
Non-polymers3585
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-50 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.638, 237.049, 210.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Protein kinase C-binding protein 1 / Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Rack7 / Zinc ...Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Rack7 / Zinc finger MYND domain-containing protein 8


Mass: 15058.151 Da / Num. of mol.: 6
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.59 Å3/Da / Density % sol: 73.22 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 1M ammonium sulfate -- 0.1M MES pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→64.15 Å / Num. obs: 46326 / % possible obs: 100 % / Redundancy: 10 % / Net I/σ(I): 13.6
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→78.625 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2344 5.07 %
Rwork0.2082 --
obs0.2096 46260 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→78.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 37 1 5539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095639
X-RAY DIFFRACTIONf_angle_d1.1067586
X-RAY DIFFRACTIONf_dihedral_angle_d16.2883498
X-RAY DIFFRACTIONf_chiral_restr0.055810
X-RAY DIFFRACTIONf_plane_restr0.007964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.75520.39341330.35942558X-RAY DIFFRACTION100
2.7552-2.81510.34991470.31322532X-RAY DIFFRACTION100
2.8151-2.88060.32341380.30342567X-RAY DIFFRACTION100
2.8806-2.95270.32431390.28132521X-RAY DIFFRACTION100
2.9527-3.03250.32221300.25792591X-RAY DIFFRACTION100
3.0325-3.12170.32511450.25272518X-RAY DIFFRACTION100
3.1217-3.22250.26861330.24922566X-RAY DIFFRACTION100
3.2225-3.33770.29011280.24652593X-RAY DIFFRACTION100
3.3377-3.47130.30291210.24692558X-RAY DIFFRACTION100
3.4713-3.62930.22141310.21342588X-RAY DIFFRACTION100
3.6293-3.82060.21681370.18922554X-RAY DIFFRACTION100
3.8206-4.060.19071200.17442610X-RAY DIFFRACTION100
4.06-4.37350.1861360.16012594X-RAY DIFFRACTION100
4.3735-4.81350.18781490.1622602X-RAY DIFFRACTION100
4.8135-5.50990.23311630.17592584X-RAY DIFFRACTION100
5.5099-6.94120.21881420.21192632X-RAY DIFFRACTION100
6.9412-78.65830.20441520.1972748X-RAY DIFFRACTION99
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)
14.6578-5.6637-0.71727.76940.74951.2405-0.9248-0.36481.1114-0.14511.9578-2.7236-1.04931.2639-0.75480.6608-0.0866-0.05270.5587-0.07190.585234.7693166.157487.6639
21.5616-0.5821-0.37794.9938-0.722-0.3633-0.07080.05270.66830.8724-0.1641-2.38-0.49590.00580.31590.9369-0.1079-0.11230.43560.10820.995739.5542109.431193.9428
36.98592.30650.33575.7575-1.88029.0181-0.4420.7767-0.5873-0.27680.1015-0.43580.32140.0180.29990.4189-0.02790.07370.3663-0.05990.387424.254765.196299.7723
4-1.2114-0.403-0.06832.5127-0.5724-1.05930.01870.036-0.03210.0291-0.08371.3183-0.0564-0.02780.07271.1270.04330.05230.564-0.16461.221119.0951126.347784.1378
59.6442-5.08933.59226.23910.27726.6839-0.2207-0.5038-0.280.43990.19810.1040.35280.31050.06640.31640.02770.09290.4594-0.00460.319432.363965.428175.0566
62.5092.1121.64211.9791.16111.38060.3161.69161.7698-0.3643-0.9682-0.58130.04080.18880.71130.80760.21510.10351.31450.34570.864244.179261.897562.2476
7-0.5108-0.782-0.03013.00510.1786-2.7716-0.1718-0.06460.134-0.77890.3756-0.7514-0.1359-0.0535-0.12632.10970.05150.12910.5243-0.02010.76731.7071111.983558.4906
82.2549-2.8967-0.68256.18830.51393.2256-0.03740.3743-1.03630.233-0.22771.27360.008-0.89430.31330.29040.01860.03270.578-0.04950.623912.8893171.033365.6597
9-0.5099-0.41230.27682.5374-0.9822-0.7917-0.2089-0.1093-0.06130.10930.38540.1029-0.0224-0.0426-0.10151.08870.04880.07660.40490.01280.684828.7544126.129293.9806
107.5889-4.46755.97143.8033-5.4278.0445-0.1875-0.20320.6896-0.12250.1209-0.49690.00970.30750.04250.5320.07630.12760.4799-0.00080.587243.163765.6161104.5095
116.9377-5.79851.69665.9062-1.16279.47020.2282-0.28530.55140.80070.00111.6379-0.9335-1.437-0.3430.38150.0160.13330.8329-0.07990.591925.005678.293349.5754
120.60310.73110.52053.15692.04213.17110.03620.1323-0.54960.6857-0.2160.48871.6528-0.4930.28731.1083-0.16110.13580.471-0.13020.816523.4379141.283960.0663
135.8323.4235-0.83572.738-2.03894.8995-0.06320.4476-0.16350.05390.0393-0.23330.02530.32510.13280.30840.05770.01330.5025-0.00290.282633.1156175.681464.7132
14-0.46710.3739-0.02729.15240.6715-0.5873-0.16920.1234-0.06650.33040.3583-0.3015-0.02950.0173-0.21.0235-0.0105-0.00850.4273-0.03060.630128.6595126.505481.7746
154.28824.43964.63178.3163.33344.7828-0.2777-0.17220.4151-0.14710.14130.1788-0.245-0.74730.20550.2897-0.01680.09280.4997-0.04020.514514.104367.574568.1902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1002 through 1024 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1025 through 1074 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1075 through 1114 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1004 through 1074 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1075 through 1114 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 1005 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1006 through 1074 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1075 through 1114 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1004 through 1074 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1075 through 1114 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1004 through 1031 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1032 through 1086 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1087 through 1114 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1004 through 1074 )
15X-RAY DIFFRACTION15chain 'F' and (resid 1075 through 1114 )

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