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- PDB-6p66: The crystal structure of the XPB complex with Bax1 from Archaeogl... -

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Basic information

Entry
Database: PDB / ID: 6p66
TitleThe crystal structure of the XPB complex with Bax1 from Archaeoglobus fulgidus at 3.0 Angstrom resolution
Components
  • DNA endonuclease Bax1
  • DNA repair protein RAD25
KeywordsHYDROLASE / Helicase / nuclease / complex
Function / homology
Function and homology information


catalytic activity, acting on DNA / DNA 3'-5' helicase / helicase activity / endonuclease activity / Hydrolases; Acting on ester bonds / hydrolase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function
Protein of unknown function DUF790, endonuclease-like / Protein of unknown function (DUF790) / Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Restriction Endonuclease - #30 / : / Restriction Endonuclease / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain ...Protein of unknown function DUF790, endonuclease-like / Protein of unknown function (DUF790) / Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Restriction Endonuclease - #30 / : / Restriction Endonuclease / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA 3'-5' translocase XPB / Endonuclease Bax1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDuPrez, K.T. / Fan, L. / Hilario, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108893 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of the XPB-Bax1 complex as a dynamic helicase-nuclease machinery for DNA repair.
Authors: DuPrez, K. / He, F. / Chen, Z. / Hilario, E. / Fan, L.
History
DepositionJun 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD25
B: DNA endonuclease Bax1
C: DNA repair protein RAD25
D: DNA endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,4957
Polymers217,3884
Non-polymers1063
Water1,982110
1
A: DNA repair protein RAD25
B: DNA endonuclease Bax1
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The mixture of XPB and Bax1 eluted at a different volume than the individual proteins., isothermal titration calorimetry, ITC experiments showed a nanomolar scale Kd value for the interaction.
  • 109 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)108,7654
Polymers108,6942
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area47720 Å2
MethodPISA
2
C: DNA repair protein RAD25
D: DNA endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7303
Polymers108,6942
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-14 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.600, 129.840, 108.150
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA repair protein RAD25


Mass: 53885.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_0358 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3) / References: UniProt: O29889
#2: Protein DNA endonuclease Bax1


Mass: 54808.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_0357 / Plasmid: pET15 / Details (production host): 6xHis removed / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O29890
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1:1 ratio of protein to mother liquor (0.1 M sodium acetate pH 4.8, 1.8 M sodium acetate)
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2015 / Details: Ni plated Invar mirror
RadiationMonochromator: Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→107.969 Å / Num. all: 52884 / Num. obs: 52884 / % possible obs: 98.5 % / Redundancy: 3.5 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Rsym value: 0.067 / Net I/av σ(I): 6.9 / Net I/σ(I): 8.4 / Num. measured all: 182895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.163.60.671.12738576640.4720.9080.671.498.4
3.16-3.353.60.4221.82594272950.30.5740.4222.198.5
3.35-3.593.50.2381.92430868810.1690.320.2383.698.7
3.59-3.873.50.1384.32241163840.0980.1850.1385.598.6
3.87-4.243.50.0867.32038658770.0620.1160.0867.998.8
4.24-4.743.40.06210.21826753360.0450.0840.06211.498.8
4.74-5.483.40.05810.61603047210.0420.0780.05813.498.7
5.48-6.713.20.056111276739930.0410.0760.05615.598.9
6.71-9.493.10.03514.8951430830.0240.0440.03525.698.3
9.49-39.9323.60.03416.3588516500.0220.0420.03429.894.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLM7.2.0data reduction
SCALA3.3.22data scaling
Coot0.8.1model building
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FWR

2fwr


Resolution: 3→39.932 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2399 5288 10 %
Rwork0.2251 --
obs0.2266 52873 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 271.2 Å2 / Biso mean: 116.0327 Å2 / Biso min: 49.29 Å2
Refinement stepCycle: final / Resolution: 3→39.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 3 110 13249
Biso mean--146.09 92.45 -
Num. residues----1837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03410.38221730.34961553172698
3.0341-3.06980.38051750.34191574174998
3.0698-3.10720.37971740.34391574174898
3.1072-3.14650.36431770.32761594177198
3.1465-3.18790.35131760.34381577175398
3.1879-3.23150.33231770.31491597177498
3.2315-3.27770.32161760.31031582175898
3.2777-3.32660.33191760.29541584176098
3.3266-3.37850.33591740.29551569174398
3.3785-3.43390.31511740.28161564173898
3.4339-3.49310.31881780.28421601177999
3.4931-3.55660.27891730.26731553172699
3.5566-3.62490.26931790.26591607178698
3.6249-3.69890.29471760.25861588176498
3.6989-3.77920.2981750.24621582175798
3.7792-3.86710.28091780.24241599177799
3.8671-3.96370.24931760.24541575175199
3.9637-4.07080.27691750.22941577175298
4.0708-4.19040.23231760.22251582175898
4.1904-4.32550.21471800.19921619179999
4.3255-4.47990.21121760.20471584176099
4.4799-4.65910.19521770.19131592176999
4.6591-4.87070.18671750.18711580175598
4.8707-5.1270.21121790.20231610178999
5.127-5.44750.22741760.21421586176298
5.4475-5.86690.25951760.23561581175799
5.8669-6.45510.2451790.23871610178999
6.4551-7.38410.24041760.22171587176398
7.3841-9.28380.18511810.17221625180698
9.2838-39.93570.1861750.18621579175495
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)
12.82010.01450.38852.8291-0.83453.4431-0.0338-0.06820.08380.33080.0076-0.1120.0621-0.0076-0.03970.4749-0.19620.04870.6325-0.14810.62026.54328.941325.328
22.21410.23840.96111.4765-0.22241.8250.0614-0.6732-0.21290.79970.0094-0.2456-0.0915-0.3619-0.01531.0508-0.1585-0.10250.82240.1390.888625.309545.813925.4955
34.62270.67250.14942.6874-0.15743.70180.03560.03740.17330.2324-0.01750.2269-0.1253-0.2377-0.04390.4916-0.2031-0.0280.5934-0.01210.667321.157754.12277.038
40.7308-0.09160.26591.15971.22343.671-0.1637-0.0265-0.03590.43080.0410.0024-0.1137-0.40770.08381.0986-0.2184-0.02490.68640.02490.702633.130969.254624.1155
50.2881-1.69310.50311.2139-0.7206-0.28620.00110.3912-0.41670.19720.04040.4970.12640.4283-0.0071.664-0.056-0.18751.57270.12311.455-8.343297.192122.5346
62.10720.39581.32740.69280.7593.707-0.0360.07280.1472-0.07280.16840.0552-0.3955-0.0046-0.11080.6491-0.26630.08730.60090.05590.7111-29.510522.283512.4171
72.5971-0.5143-1.27072.11510.09242.74070.37770.34030.3099-0.42420.0469-0.0594-0.3930.0421-0.2951.1253-0.01520.08230.58520.01380.6915-51.761134.1325.9007
83.19630.9611-0.22852.28990.29593.14360.0985-0.53710.52730.1253-0.1203-0.1908-0.33030.12280.07681.1014-0.06530.03480.8013-0.23660.7542-48.987540.958540.3545
90.3560.08190.23012.4192-1.54482.45520.1407-0.04390.06670.1051-0.12970.34130.2752-0.09250.0640.78990.19090.07730.8159-0.03960.6817-64.843653.531929.3661
101.06361.11261.21911.351-0.1342.87670.2978-0.44030.26130.6071-0.33630.0447-0.6891-0.09550.03261.11070.04950.03421.1798-0.07540.8186-52.742575.962829.4823
110.52960.578-0.02650.33560.18980.5774-0.1371-0.2184-0.11240.3391-0.1057-1.2583-0.45041.04810.0981.4901-0.1525-0.12572.2309-0.05381.4805-35.113382.86134.2086
121.13710.4941-0.42312.37422.10092.37180.1285-0.2999-0.2506-0.0421-0.02210.03360.4676-0.0649-0.08611.3524-0.2092-0.07851.004-0.00911.1547-25.4034124.389914.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 228 )A3 - 228
2X-RAY DIFFRACTION2chain 'A' and (resid 229 through 311 )A229 - 311
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 445 )A312 - 445
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 247 )B1 - 247
5X-RAY DIFFRACTION5chain 'B' and (resid 248 through 467 )B248 - 467
6X-RAY DIFFRACTION6chain 'C' and (resid -16 through 228 )C-16 - 228
7X-RAY DIFFRACTION7chain 'C' and (resid 229 through 338 )C229 - 338
8X-RAY DIFFRACTION8chain 'C' and (resid 339 through 443 )C339 - 443
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 245 )D1 - 245
10X-RAY DIFFRACTION10chain 'D' and (resid 246 through 338 )D246 - 338
11X-RAY DIFFRACTION11chain 'D' and (resid 339 through 398 )D339 - 398
12X-RAY DIFFRACTION12chain 'D' and (resid 399 through 467 )D399 - 467

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