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- PDB-4cos: Crystal structure of the PHD-Bromo-PWWP cassette of human PRKCBP1 -

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Basic information

Entry
Database: PDB / ID: 4cos
TitleCrystal structure of the PHD-Bromo-PWWP cassette of human PRKCBP1
ComponentsPROTEIN KINASE C-BINDING PROTEIN 1
KeywordsTRANSCRIPTION / PHD DOMAIN / BROMO DOMAIN / PWWP DOMAIN
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
1,4-DIETHYLENE DIOXIDE / MYND-type zinc finger-containing chromatin reader ZMYND8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsKrojer, T. / Savitsky, P. / Newman, J.A. / Cooper, C.D.O. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Filippakopoulos, P.
CitationJournal: Cell Rep / Year: 2016
Title: Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin.
Authors: Savitsky, P. / Krojer, T. / Fujisawa, T. / Lambert, J.P. / Picaud, S. / Wang, C.Y. / Shanle, E.K. / Krajewski, K. / Friedrichsen, H. / Kanapin, A. / Goding, C. / Schapira, M. / Samsonova, A. ...Authors: Savitsky, P. / Krojer, T. / Fujisawa, T. / Lambert, J.P. / Picaud, S. / Wang, C.Y. / Shanle, E.K. / Krajewski, K. / Friedrichsen, H. / Kanapin, A. / Goding, C. / Schapira, M. / Samsonova, A. / Strahl, B.D. / Gingras, A.C. / Filippakopoulos, P.
History
DepositionJan 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2066
Polymers37,8341
Non-polymers3725
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.955, 68.835, 70.350
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 / PRKCBP1 / CUTANEOUS T-CELL LYMPHOMA-ASSOCIATED ANTIGEN SE14-3 CTCL-ASSOCIATED ANTIGEN SE14-3 / ...PRKCBP1 / CUTANEOUS T-CELL LYMPHOMA-ASSOCIATED ANTIGEN SE14-3 CTCL-ASSOCIATED ANTIGEN SE14-3 / RACK7 / ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 8


Mass: 37833.730 Da / Num. of mol.: 1 / Fragment: PHD-BROMO-PWWP DOMAIN, RESIDUES 83-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.14 Å3/Da / Density % sol: 42.7 % / Description: NONE
Crystal growpH: 6.3 / Details: pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.67→49.2 Å / Num. obs: 38079 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.67→49.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.168 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21039 1900 5 %RANDOM
Rwork0.17589 ---
obs0.17753 36091 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--2.4 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.67→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 15 333 2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192656
X-RAY DIFFRACTIONr_bond_other_d0.0020.022455
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9513604
X-RAY DIFFRACTIONr_angle_other_deg0.8673.0045667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1922.2661281
X-RAY DIFFRACTIONr_mcbond_other2.1192.2641280
X-RAY DIFFRACTIONr_mcangle_it3.1883.3841608
X-RAY DIFFRACTIONr_mcangle_other3.1873.3871609
X-RAY DIFFRACTIONr_scbond_it2.9362.6341375
X-RAY DIFFRACTIONr_scbond_other2.9352.6361376
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5563.7971994
X-RAY DIFFRACTIONr_long_range_B_refined7.27320.4313410
X-RAY DIFFRACTIONr_long_range_B_other7.12219.6933267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.675→1.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 158 -
Rwork0.335 2603 -
obs--98.64 %
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)
11.2376-0.7265-0.17490.45170.11470.03060.19990.21550.1214-0.1086-0.1811-0.0867-0.0244-0.0582-0.01880.03310.01950.01870.17260.06080.061422.59743.1674.597
20.88370.0779-0.52760.0799-0.19650.8041-0.014-0.01790.013-0.02320.05480.00580.0315-0.024-0.04080.0101-0.02290.00580.08220.01540.048429.80627.1637.674
30.5787-0.01510.13420.3027-0.23150.5596-0.0616-0.0877-0.0116-0.05010.0132-0.03460.0152-0.10520.04840.01590.01290.00730.0706-0.00940.044360.79939.8042.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 149
2X-RAY DIFFRACTION2A150 - 264
3X-RAY DIFFRACTION3A265 - 399

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