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- PDB-1pcf: HUMAN TRANSCRIPTIONAL COACTIVATOR PC4 C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1pcf
TitleHUMAN TRANSCRIPTIONAL COACTIVATOR PC4 C-TERMINAL DOMAIN
ComponentsTRANSCRIPTIONAL COACTIVATOR PC4
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL COFACTOR / TRANSCRIPTIONAL CO-ACTIVATOR / SSDNA BINDING / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of DNA metabolic process / negative regulation of DNA duplex unwinding / RNA polymerase II promoter clearance / positive regulation of transcription initiation by RNA polymerase II / single-stranded DNA binding / transcription regulator complex / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleolus / regulation of transcription by RNA polymerase II ...negative regulation of DNA metabolic process / negative regulation of DNA duplex unwinding / RNA polymerase II promoter clearance / positive regulation of transcription initiation by RNA polymerase II / single-stranded DNA binding / transcription regulator complex / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleolus / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
RNA polymerase II transcriptional coactivator Sub1/Tcp4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Activated RNA polymerase II transcriptional coactivator p15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.74 Å
AuthorsBrandsen, J. / Gros, P.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: C-terminal domain of transcription cofactor PC4 reveals dimeric ssDNA binding site.
Authors: Brandsen, J. / Werten, S. / van der Vliet, P.C. / Meisterernst, M. / Kroon, J. / Gros, P.
History
DepositionSep 9, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL COACTIVATOR PC4
B: TRANSCRIPTIONAL COACTIVATOR PC4
C: TRANSCRIPTIONAL COACTIVATOR PC4
D: TRANSCRIPTIONAL COACTIVATOR PC4
E: TRANSCRIPTIONAL COACTIVATOR PC4
F: TRANSCRIPTIONAL COACTIVATOR PC4
G: TRANSCRIPTIONAL COACTIVATOR PC4
H: TRANSCRIPTIONAL COACTIVATOR PC4


Theoretical massNumber of molelcules
Total (without water)62,2728
Polymers62,2728
Non-polymers00
Water7,819434
1
A: TRANSCRIPTIONAL COACTIVATOR PC4
B: TRANSCRIPTIONAL COACTIVATOR PC4


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-26 kcal/mol
Surface area8190 Å2
MethodPISA
2
C: TRANSCRIPTIONAL COACTIVATOR PC4
D: TRANSCRIPTIONAL COACTIVATOR PC4


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-26 kcal/mol
Surface area8160 Å2
MethodPISA
3
E: TRANSCRIPTIONAL COACTIVATOR PC4
F: TRANSCRIPTIONAL COACTIVATOR PC4


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area8180 Å2
MethodPISA
4
G: TRANSCRIPTIONAL COACTIVATOR PC4
H: TRANSCRIPTIONAL COACTIVATOR PC4


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.283, 67.814, 67.170
Angle α, β, γ (deg.)87.69, 84.37, 85.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95721, -0.148412, 0.248442), (-0.166878, -0.41831, -0.892843), (0.236434, -0.896097, 0.375644)70.7556, 148.7375, 84.3861
2given(0.96765, -0.200512, -0.15313), (0.14018, -0.077347, 0.9871), (-0.20977, -0.976633, -0.046737)15.0308, -46.0331, 136.974
3given(-0.998872, -0.035171, -0.031883), (-0.022192, 0.939681, -0.341331), (0.041965, -0.340239, -0.939402)99.208, 42.4145, 179.3701
4given(0.98155, -0.013781, -0.190706), (-0.021136, -0.999107, -0.036585), (-0.190031, 0.039941, -0.980965)0.3304, 81.4715, 173.1833
5given(-0.980983, 0.186876, -0.052431), (0.017002, 0.351836, 0.935907), (0.193346, 0.917218, -0.348323)100.7074, -40.3376, 72.3411
6given(0.995407, 0.075178, -0.059274), (-0.059633, 0.002541, -0.998217), (-0.074894, 0.997167, 0.007012)-23.7922, 123.0693, 50.1213
7given(-0.961603, 0.173417, 0.212712), (-0.076437, -0.913627, 0.399303), (0.263585, 0.367712, 0.891802)87.3557, 58.4553, -12.8508

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Components

#1: Protein
TRANSCRIPTIONAL COACTIVATOR PC4 / P15


Mass: 7784.024 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P53999
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.9 Å3/Da / Density % sol: 59 %
Crystal growpH: 4.6
Details: PROTEIN WAS CRYSTALLIZED FROM 25% MPD, 200 MM NACL AND 100 MM NAAC BUFFER (PH 4.6)
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %(v/v)MPD12
20.2 M12NaCl
30.1 Msodium acetate12
47-10 mg/mlprotein11
510 mMHEPES11
60.2 M11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9117
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 69529 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.229 / % possible all: 83.4
Reflection
*PLUS
Num. measured all: 177425 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 83.4 %

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Processing

Software
NameClassification
SHARPphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.74→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3495 5 %SHELL
Rwork0.197 ---
all-69529 --
obs-69529 93.4 %-
Displacement parametersBiso mean: 21.5 Å2
Refine analyzeLuzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 0 434 4794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it2.0353
X-RAY DIFFRACTIONp_mcangle_it2.7735
X-RAY DIFFRACTIONp_scbond_it4.7526
X-RAY DIFFRACTIONp_scangle_it6.828
X-RAY DIFFRACTIONp_plane_restr0.0310.04
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.3
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor16.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.920
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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