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- PDB-6c8c: Chimeric Pol kappa RIR Rev1 C-terminal domain in complex with JHRE06 -

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Basic information

Entry
Database: PDB / ID: 6c8c
TitleChimeric Pol kappa RIR Rev1 C-terminal domain in complex with JHRE06
ComponentsChimeric protein of the Pol Kappa RIR helix and the Rev1 C-terminal domainChimera
KeywordsREPLICATION / translesion synthesis / DNA damage tolerance / Rev1
Function / homology
Function and homology information


Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / deoxycytidyl transferase activity ...Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / site of DNA damage / error-prone translesion synthesis / response to UV / cellular response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / molecular adaptor activity / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / DNA polymerase IV ...DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / DNA polymerase IV / DNApol eta/Rev1, HhH motif / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / BRCA1 C Terminus (BRCT) domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EQ7 / DNA repair protein REV1 / DNA polymerase kappa
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNajeeb, J. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA191448 United States
CitationJournal: Cell / Year: 2019
Title: A Small Molecule Targeting Mutagenic Translesion Synthesis Improves Chemotherapy.
Authors: Wojtaszek, J.L. / Chatterjee, N. / Najeeb, J. / Ramos, A. / Lee, M. / Bian, K. / Xue, J.Y. / Fenton, B.A. / Park, H. / Li, D. / Hemann, M.T. / Hong, J. / Walker, G.C. / Zhou, P.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Chimeric protein of the Pol Kappa RIR helix and the Rev1 C-terminal domain
B: Chimeric protein of the Pol Kappa RIR helix and the Rev1 C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0043
Polymers27,5362
Non-polymers4691
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-6 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.550, 51.020, 98.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chimeric protein of the Pol Kappa RIR helix and the Rev1 C-terminal domain / Chimera / DINB protein / DINP / Rev1-like terminal deoxycytidyl transferase


Mass: 13767.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polk, Dinb1, Rev1, Rev1l / Production host: Escherichia coli (E. coli)
References: UniProt: Q9QUG2, UniProt: Q920Q2, DNA-directed DNA polymerase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-EQ7 / 8-chloro-2-[(2,4-dichlorophenyl)amino]-3-(3-methylbutanoyl)-5-nitroquinolin-4(1H)-one


Mass: 468.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16Cl3N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: HEPES pH 7.0, potassium chloride, 2-Methyl-2,4-pentanediol (MPD) beta-mercaptoethanol, PEG 3350, magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97779 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.5→45.344 Å / Num. obs: 40049 / % possible obs: 99.8 % / Redundancy: 7.73 % / Rrim(I) all: 0.077 / Net I/σ(I): 16.5
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4.83 % / Num. unique obs: 2888 / Rrim(I) all: 0.457 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C59

6c59


Resolution: 1.5→35.171 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.191 2007 5.01 %
Rwork0.1637 --
obs0.1651 40047 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 30 421 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062010
X-RAY DIFFRACTIONf_angle_d0.7722733
X-RAY DIFFRACTIONf_dihedral_angle_d3.9051663
X-RAY DIFFRACTIONf_chiral_restr0.044309
X-RAY DIFFRACTIONf_plane_restr0.004349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.21951260.20012655X-RAY DIFFRACTION100
1.5375-1.57910.18291370.16842689X-RAY DIFFRACTION100
1.5791-1.62560.18511660.16792656X-RAY DIFFRACTION100
1.6256-1.6780.22931370.16242708X-RAY DIFFRACTION100
1.678-1.7380.23281350.17392697X-RAY DIFFRACTION100
1.738-1.80760.21071480.17362675X-RAY DIFFRACTION100
1.8076-1.88990.21171360.16792708X-RAY DIFFRACTION100
1.8899-1.98950.18911280.16622691X-RAY DIFFRACTION100
1.9895-2.11410.19571340.16062737X-RAY DIFFRACTION100
2.1141-2.27730.20491290.15982712X-RAY DIFFRACTION100
2.2773-2.50650.18481830.17032688X-RAY DIFFRACTION100
2.5065-2.8690.19071350.17082746X-RAY DIFFRACTION100
2.869-3.61410.18361520.15392765X-RAY DIFFRACTION100
3.6141-35.18050.17171610.15612913X-RAY DIFFRACTION100
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)
10.42920.4485-0.0160.8559-0.5280.7754-0.1491-0.1472-0.7369-0.18320.0214-0.47060.26580.0145-0.03780.0983-0.0061-0.00250.13250.06520.2862-5.8167-45.3294-4.4276
20.30160.0847-0.95250.1119-0.06693.1732-0.0910.6338-0.1388-0.285-0.08210.09180.7405-0.3535-0.08340.15930.0171-0.05750.20070.01650.36066.7332-44.9745-0.6614
30.51820.184-0.27811.0667-0.49450.5932-0.20480.0807-0.5495-0.3716-0.0098-0.29080.4581-0.0923-0.12670.1013-0.04950.02930.1031-0.03190.1931-3.1013-38.3549-12.5821
40.28170.1920.09360.12460.11780.05910.0538-0.3577-0.16920.118-0.1929-0.0784-0.0036-0.0176-0.060.0714-0.0317-0.02210.11340.05050.1197-2.4635-31.3045-3.7383
50.57140.14810.05840.20840.10310.44080.01120.1772-0.2737-0.1036-0.01-0.1410.00060.0379-0.04840.09-0.027-0.00760.1240.02320.0826-2.4126-28.2867-15.5638
60.3047-0.0606-0.13370.19190.09230.32510.09-0.07620.18730.0121-0.13540.1351-0.1429-0.0920.00920.0944-0.02840.00280.1090.00950.0782-8.1537-23.6238-7.6434
70.05530.1182-0.01180.41620.18140.17050.1542-0.11940.04910.3147-0.05650.02870.0971-0.1582-0.00450.1523-0.0620.03530.1676-0.01930.12242.8466-10.839-5.0639
80.20240.01590.1610.00880.06450.90010.12480.3771-0.0962-0.4238-0.0417-0.68710.07270.05940.05310.13710.01770.06160.1902-0.00940.314931.9849-8.9711-24.6178
90.04130.0155-0.01360.15890.04580.0006-0.02630.0492-0.2250.14850.0437-0.21780.19630.09630.00130.13250.00450.00840.0993-0.02730.120525.4019-17.7552-19.4844
100.2893-0.4437-0.06760.8648-0.26081.19130.00920.00440.06960.1236-0.0491-0.0915-0.03430.124-0.0660.0834-0.0255-0.01410.06760.00460.061821.36-6.7857-17.1618
110.4786-0.21210.02220.49530.00360.179-0.0622-0.1580.10990.08040.04920.247-0.2460.0395-0.00980.1655-0.03210.00640.0931-0.01490.060917.7003-4.7871-7.6102
120.1060.1214-0.13010.24-0.41130.6220.0621-0.07170.2654-0.0211-0.00790.3008-0.0824-0.10220.00520.1102-0.0170.01880.08080.00950.12229.0034-3.1018-14.1093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 111 )
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 119 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 91 )
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 119 )

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