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- PDB-7e4w: Human Transcriptional Co-activator PC4 (C-terminal Domain) in spa... -

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Basic information

Entry
Database: PDB / ID: 7e4w
TitleHuman Transcriptional Co-activator PC4 (C-terminal Domain) in space group P1211
ComponentsActivated RNA polymerase II transcriptional coactivator p15
KeywordsTRANSCRIPTION / HUMAN TRANSCRIPTIONAL COACTIVATOR PC4
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) / ssDNA-binding transcriptional regulator
Similarity search - Domain/homology
Activated RNA polymerase II transcriptional coactivator p15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDev, A. / Pandey, B. / Basu, G.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/Med-II/NIBMG/SyMeC/2014/Vol.II India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules.
Authors: Pandey, B. / Dev, A. / Chakravorty, D. / Bhandare, V.V. / Polley, S. / Roy, S. / Basu, G.
History
DepositionFeb 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activated RNA polymerase II transcriptional coactivator p15
B: Activated RNA polymerase II transcriptional coactivator p15
C: Activated RNA polymerase II transcriptional coactivator p15
D: Activated RNA polymerase II transcriptional coactivator p15
E: Activated RNA polymerase II transcriptional coactivator p15
F: Activated RNA polymerase II transcriptional coactivator p15
G: Activated RNA polymerase II transcriptional coactivator p15
H: Activated RNA polymerase II transcriptional coactivator p15
I: Activated RNA polymerase II transcriptional coactivator p15
J: Activated RNA polymerase II transcriptional coactivator p15
K: Activated RNA polymerase II transcriptional coactivator p15
L: Activated RNA polymerase II transcriptional coactivator p15
M: Activated RNA polymerase II transcriptional coactivator p15
N: Activated RNA polymerase II transcriptional coactivator p15
O: Activated RNA polymerase II transcriptional coactivator p15
P: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)124,54416
Polymers124,54416
Non-polymers00
Water2,360131
1
A: Activated RNA polymerase II transcriptional coactivator p15
B: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-24 kcal/mol
Surface area8160 Å2
MethodPISA
2
C: Activated RNA polymerase II transcriptional coactivator p15
D: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-26 kcal/mol
Surface area8130 Å2
MethodPISA
3
E: Activated RNA polymerase II transcriptional coactivator p15
F: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-23 kcal/mol
Surface area8060 Å2
MethodPISA
4
G: Activated RNA polymerase II transcriptional coactivator p15
H: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area8070 Å2
MethodPISA
5
I: Activated RNA polymerase II transcriptional coactivator p15
J: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area8180 Å2
MethodPISA
6
K: Activated RNA polymerase II transcriptional coactivator p15
L: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-25 kcal/mol
Surface area8320 Å2
MethodPISA
7
M: Activated RNA polymerase II transcriptional coactivator p15
N: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23 kcal/mol
Surface area8100 Å2
MethodPISA
8
O: Activated RNA polymerase II transcriptional coactivator p15
P: Activated RNA polymerase II transcriptional coactivator p15


Theoretical massNumber of molelcules
Total (without water)15,5682
Polymers15,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.012, 166.844, 108.309
Angle α, β, γ (deg.)90.000, 93.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Activated RNA polymerase II transcriptional coactivator p15 / Positive cofactor 4 / PC4 / SUB1 homolog / p14


Mass: 7784.024 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: Human Transcription Coactivator / Source: (gene. exp.) Homo sapiens (human) / Gene: SUB1, PC4, RPO2TC1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P53999
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.55 Å3/Da / Density % sol: 60 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 285 K / Method: vapor diffusion
Details: 20% MPD, 150-200 MM NACL, Phosphate Buffer (PH 5-5.2)
PH range: 5-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 2, 2019
RadiationMonochromator: PX-BL21 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.9→108.13 Å / Num. obs: 38333 / % possible obs: 99.53 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.79 Å2 / CC1/2: 0.988 / CC star: 0.997 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.41 / Num. unique obs: 3798 / CC1/2: 0.614 / % possible all: 99.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata processing
Aimlessdata scaling
PHENIXmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PCF

1pcf


Resolution: 2.9→108.13 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.856 / SU B: 19.244 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.79 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1868 4.9 %RANDOM
Rwork0.2277 ---
obs0.2301 36465 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.71 Å2 / Biso mean: 47.565 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.47 Å20 Å2-1.05 Å2
2---1.92 Å20 Å2
3----2.41 Å2
Refinement stepCycle: final / Resolution: 2.9→108.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8662 0 0 131 8793
Biso mean---24.34 -
Num. residues----1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198829
X-RAY DIFFRACTIONr_bond_other_d0.0020.028684
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.97511807
X-RAY DIFFRACTIONr_angle_other_deg0.935320059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55751040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02624.165425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.204151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1891577
X-RAY DIFFRACTIONr_chiral_restr0.0820.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021932
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 130 -
Rwork0.331 2677 -
all-2807 -
obs--99.93 %

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