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- PDB-2c62: Crystal Structure of the Human Transcription Cofactor PC4 in Comp... -

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Basic information

Entry
Database: PDB / ID: 2c62
TitleCrystal Structure of the Human Transcription Cofactor PC4 in Complex with Single-Stranded DNA
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3'
  • ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15
KeywordsTRANSCRIPTION / TRANSCRIPTION COFACTOR / SINGLE-STRANDED DNA / PROTEIN-DNA COMPLEX / DNA UNWINDING / ACTIVATOR / DNA-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION / TRANSCRIPTION REGULATION
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
DNA / DNA (> 10) / Activated RNA polymerase II transcriptional coactivator p15
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWerten, S. / Moras, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: A Global Transcription Cofactor Bound to Juxtaposed Strands of Unwound DNA
Authors: Werten, S. / Moras, D.
History
DepositionNov 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15
B: ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8245
Polymers21,6323
Non-polymers1922
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.242, 67.242, 131.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE BIOLOGICALLY RELEVANT STATE OF THE MOLECULE ISTHE CONTENTS OF THE ASYMMETRIC UNIT.

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Components

#1: Protein ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15 / PC4 / POSITIVE COFACTOR 4 / P14


Mass: 7784.024 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SSDNA-BINDING DOMAIN, RESIDUES 62-126
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL ALA RESIDUE RESULTS FROM VECTOR SEQUENCE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-11A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53999
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3'


Mass: 6063.912 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGENERAL COACTIVATOR THAT FUNCTIONS IN COOPERATION WITH TAFS AND MEDIATES FUNCTIONAL INTERACTIONS ...GENERAL COACTIVATOR THAT FUNCTIONS IN COOPERATION WITH TAFS AND MEDIATES FUNCTIONAL INTERACTIONS BETWEEN UPSTREAM ACTIVATORS AND THE GENERAL TRANSCRIPTIONAL MACHINERY
Sequence detailsC-TERMINAL DOMAIN ONLY, PRECEEDED BY ALA FROM EXPRESSION VECTOR SEQUENCE SYNTHETIC OLIGONUCLEOTIDE

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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: 3.33 Å3/Da / Density % sol: 62.77 %
Crystal growpH: 6.75 / Details: 0.1 M ADA PH 6.75, 1.9 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2003 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 31658 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.3
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.43 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PCF, CHAINS A AND B

1pcf


Resolution: 1.74→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1346476 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1489 4.9 %RANDOM
Rwork0.229 ---
obs0.229 30178 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.429 Å2 / ksol: 0.363232 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.74→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 323 10 176 1599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 1.74→1.8 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.367 129 5.1 %
Rwork0.31 2384 -
obs--80.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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