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- PDB-4dfc: Core UvrA/TRCF complex -

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Basic information

Entry
Database: PDB / ID: 4dfc
TitleCore UvrA/TRCF complex
Components
  • Transcription-repair-coupling factor
  • UvrABC system protein A
KeywordsHydrolase/DNA binding protein / alpha/beta domains / DNA repair / ATP Binding / DNA binding / nucleotide excision repair / Hydrolase-DNA binding protein complex
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / excinuclease ABC activity / excinuclease repair complex / RNA polymerase core enzyme binding / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / DNA repair complex / SOS response / transcription-coupled nucleotide-excision repair / nucleotide-excision repair ...transcription-coupled nucleotide-excision repair, DNA damage recognition / excinuclease ABC activity / excinuclease repair complex / RNA polymerase core enzyme binding / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / DNA repair complex / SOS response / transcription-coupled nucleotide-excision repair / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to radiation / damaged DNA binding / hydrolase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / : / MFD, D3 domain / Ribosomal protein L1/L10, rRNA-binding domain ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / : / MFD, D3 domain / Ribosomal protein L1/L10, rRNA-binding domain / : / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein A / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsDeaconescu, A.M. / Grigorieff, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface.
Authors: Deaconescu, A.M. / Sevostyanova, A. / Artsimovitch, I. / Grigorieff, N.
History
DepositionJan 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription-repair-coupling factor
B: UvrABC system protein A
C: Transcription-repair-coupling factor
D: UvrABC system protein A


Theoretical massNumber of molelcules
Total (without water)49,0844
Polymers49,0844
Non-polymers00
Water0
1
A: Transcription-repair-coupling factor
B: UvrABC system protein A


Theoretical massNumber of molelcules
Total (without water)24,5422
Polymers24,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transcription-repair-coupling factor
D: UvrABC system protein A


Theoretical massNumber of molelcules
Total (without water)24,5422
Polymers24,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.168, 119.168, 234.334
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Transcription-repair-coupling factor / TRCF / ATP-dependent helicase mfd


Mass: 10578.898 Da / Num. of mol.: 2 / Fragment: TRCF-D2 Domain, UNP residues 127-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1114, Escherichia coli, JW1100, mfd / Plasmid: pET28a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: P30958, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein UvrABC system protein A / UvrA protein / Excinuclease ABC subunit A


Mass: 13962.887 Da / Num. of mol.: 2 / Fragment: UNP residues 131-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4058, dinE, Escherichia coli, JW4019, uvrA / Plasmid: pET28a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P0A698, EC: 3.6.1.3

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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: 4.89 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 10% PEG3350, 4% Tacsimate pH 4.8 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 24835 / Num. obs: 24835 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.8→2.85 Å / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPN

3fpn


Resolution: 2.803→29.981 Å / SU ML: 0.92 / σ(F): 1.34 / Phase error: 33.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1240 5.02 %
Rwork0.2379 --
obs0.2402 24708 99.16 %
all-24835 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.016 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0361 Å20 Å2-0 Å2
2--6.0361 Å2-0 Å2
3----13.0478 Å2
Refinement stepCycle: LAST / Resolution: 2.803→29.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 0 0 3143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093183
X-RAY DIFFRACTIONf_angle_d1.344296
X-RAY DIFFRACTIONf_dihedral_angle_d18.1911198
X-RAY DIFFRACTIONf_chiral_restr0.09498
X-RAY DIFFRACTIONf_plane_restr0.006567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.91530.49191330.41222501X-RAY DIFFRACTION97
2.9153-3.04790.40811340.3352547X-RAY DIFFRACTION99
3.0479-3.20840.39691360.2882554X-RAY DIFFRACTION99
3.2084-3.40920.31821370.27532583X-RAY DIFFRACTION100
3.4092-3.67190.36021340.2782567X-RAY DIFFRACTION99
3.6719-4.04070.29031370.2432595X-RAY DIFFRACTION99
4.0407-4.62350.22041380.18452632X-RAY DIFFRACTION100
4.6235-5.81820.24551420.20512664X-RAY DIFFRACTION100
5.8182-29.9830.25061490.22732825X-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)
15.1741-1.6326-0.43155.64162.83224.92640.017-0.853-0.58450.33220.00670.40150.024-0.01850.02160.7665-0.0503-0.02730.82380.0720.427855.2918-52.100221.4952
21.99130.4720.83094.0522-0.32135.44460.2111-0.3840.38830.533-0.36530.3399-0.131-1.32660.08930.43240.03520.07420.9195-0.16460.331946.3219-32.685218.5174
38.0777-0.24481.89836.88040.66374.2004-0.20510.61370.38170.52410.6733-0.9017-0.37892.2157-0.43570.6925-0.2398-0.14731.3606-0.09040.621193.9996-30.223313.5778
43.7447-1.8442-2.12985.0812-1.73087.10270.1474-0.02670.1559-0.07020.0317-0.0397-0.2862-0.1651-0.18210.44670.025-0.09170.6174-0.07160.256373.8704-36.289514.6188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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