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- PDB-4ern: Crystal structure of the C-terminal domain of human XPB/ERCC-3 ex... -

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Basic information

Entry
Database: PDB / ID: 4ern
TitleCrystal structure of the C-terminal domain of human XPB/ERCC-3 excision repair protein at 1.80 A
ComponentsTFIIH basal transcription factor complex helicase XPB subunit
KeywordsHYDROLASE / Helicase domain 2 / general transcription factor TFIIH / nucleotide excision repair / transcription coupled repair / basal transcription / nucleus
Function / homology
Function and homology information


nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / UV protection / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition ...nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / UV protection / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / 3'-5' DNA helicase activity / RNA Polymerase I Transcription Initiation / DNA topological change / transcription factor TFIID complex / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / NoRC negatively regulates rRNA expression / protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / positive regulation of apoptotic process / DNA repair / apoptotic process / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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. ...Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase/translocase subunit XPB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHilario, E. / Li, Y. / Fan, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE.
Authors: Hilario, E. / Li, Y. / Nobumori, Y. / Liu, X. / Fan, L.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFIIH basal transcription factor complex helicase XPB subunit


Theoretical massNumber of molelcules
Total (without water)33,4201
Polymers33,4201
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.260, 73.650, 84.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBased on S-100 size exclusion chromatography results, ERCC3 fragment (494-782) exist as a monomer in aqueous buffer solutions.

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Components

#1: Protein TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 33420.199 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 494-782)
Source method: isolated from a genetically manipulated source
Details: Coding sequence was cloned into BamHI and SalI restriction sites.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys-S / References: UniProt: P19447, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.78 Å3/Da / Density % sol: 30.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.55
Details: 0.1 M sodium acetate, pH 5.55, 0.2 M ammonium acetate, 27% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2011 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→18.55 Å / Num. all: 22258 / Num. obs: 22258 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 30.207 Å2 / Rsym value: 0.036 / Net I/σ(I): 20.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.94.50.4881.61441431710.48897.2
1.9-2.014.60.2742.81381730120.27497.6
2.01-2.154.60.1564.91336028790.15699
2.15-2.324.70.09481289527320.09499.9
2.32-2.554.80.06411.51199224970.06499.4
2.55-2.854.90.04316.61096822360.04398.4
2.85-3.2950.02922.1981519810.02997.5
3.29-4.024.90.03417840016990.03497.5
4.02-5.694.90.02128653113430.02197.9
5.69-19.2914.70.01731.534897490.01794.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.29 Å
Translation2.5 Å19.29 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22257
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.48-100280.917501
5.15-6.4828.70.908503
4.5-5.1520.80.922501
4.07-4.517.10.935505
3.76-4.0717.50.941526
3.51-3.7618.50.922578
3.3-3.5121.90.9606
3.13-3.320.90.898649
2.98-3.1320.80.904666
2.85-2.9823.10.889705
2.73-2.8523.90.883716
2.63-2.7322.80.897780
2.54-2.6323.50.903787
2.46-2.5422.90.895819
2.39-2.4622.60.902858
2.32-2.3921.70.918885
2.25-2.3221.70.924890
2.2-2.2519.90.923945
2.14-2.222.90.918947
2.09-2.1422.90.905979
2.05-2.0922.60.91962
2-2.0522.50.921997
1.96-220.90.9341030
1.92-1.9621.60.9321031
1.89-1.9222.40.9321039
1.85-1.8924.60.9161071
1.8-1.8531.10.9111781

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.20data reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
DM6.2phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FZL

2fzl


Resolution: 1.8→18.553 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8598 / SU ML: 0.27 / Isotropic thermal model: Anisotropic / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 1134 5.09 %RANDOM
Rwork0.201 ---
obs0.2028 22258 97.84 %-
all-22299 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.999 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 153.88 Å2 / Biso mean: 42.702 Å2 / Biso min: 13.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.4851 Å20 Å20 Å2
2--0.0196 Å2-0 Å2
3---0.4655 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 86 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111963
X-RAY DIFFRACTIONf_angle_d1.3432658
X-RAY DIFFRACTIONf_chiral_restr0.103288
X-RAY DIFFRACTIONf_plane_restr0.006348
X-RAY DIFFRACTIONf_dihedral_angle_d15.77766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.88190.38621540.34612547270197
1.8819-1.9810.32721390.25482559269897
1.981-2.1050.20481340.2032637277198
2.105-2.26720.25541420.190726642806100
2.2672-2.49490.2251330.20642659279299
2.4949-2.85480.29211410.21482646278798
2.8548-3.59250.25621460.20262642278897
3.5925-18.55390.19351450.17922770291596
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)
11.34660.5624-0.51242.4702-0.49044.15410.0570.018-0.1626-0.08690.04390.117-0.33480.10570.06530.11570.0017-0.01370.12730.0110.156511.81733.7051.3845
21.71520.1848-0.28842.1648-1.34294.15390.0563-0.2592-0.4106-0.06790.06660.1060.393-0.39420.01760.1166-0.0282-0.00450.2250.07470.27348.4443-4.77098.6369
30.9094-0.8831-0.53550.9652-0.28662.21580.10780.2326-0.2978-0.14580.1060.1024-1.0919-0.05820.18420.5111-0.02240.05070.23060.02070.332911.664317.40246.4662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 502:621)A502 - 621
2X-RAY DIFFRACTION2chain 'A' and (resseq 622:705)A622 - 705
3X-RAY DIFFRACTION3chain 'A' and (resseq 706:730)A706 - 730

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