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- PDB-4ba9: The structural basis for the coordination of Y-family Translesion... -

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Basic information

Entry
Database: PDB / ID: 4ba9
TitleThe structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
ComponentsDNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
KeywordsTRANSFERASE / TLS / DNA REPAIR
Function / homology
Function and homology information


deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis ...deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol
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 type-Y, HhH motif ...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 type-Y, HhH motif / IMS family HHH motif / 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
NICKEL (II) ION / DNA polymerase kappa / DNA repair protein REV1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsGrummitt, C.G. / Kilkenny, M.L. / Frey, A. / Roe, S.M. / Oliver, A.W. / Sale, J.E. / Pearl, L.H.
CitationJournal: To be Published
Title: The Structural Basis for the Coordination of Y- Family Translesion DNA Polymerases by Rev1
Authors: Grummitt, C.G. / Kilkenny, M.L. / Frey, A. / Roe, S.M. / Oliver, A.W. / Sale, J.E. / Pearl, L.H.
History
DepositionSep 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,02624
Polymers78,2456
Non-polymers78118
Water2,864159
1
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63715
Polymers52,1634
Non-polymers47411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-116.5 kcal/mol
Surface area21940 Å2
MethodPISA
2
E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules

E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77918
Polymers52,1634
Non-polymers61514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6580 Å2
ΔGint-171.1 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.750, 105.750, 424.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 / DINB PROTEIN / DINPALPHA INTEGRIN-BINDING PROTEIN 80 / AIBP80 / REV1-LIKE TERMINAL DEOXYCYTIDYL ...DINB PROTEIN / DINPALPHA INTEGRIN-BINDING PROTEIN 80 / AIBP80 / REV1-LIKE TERMINAL DEOXYCYTIDYL TRANSFERASE / REV1


Mass: 13040.846 Da / Num. of mol.: 6 / Fragment: C-TERMINAL POLYMERASE INTERACTING DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FUSION OF HUMAN REV-1 C-TERMINAL POLYMERASE INTERACTING DOMAIN (REV1-PID) WITH THE REV-1 INTERACTING MOTIF OF POLYMERASE KAPPA (POLKAPPA-RIM).
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PTWO-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9UBT6, UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.92 Å3/Da / Density % sol: 57.84 % / Description: NONE
Crystal growDetails: 100 MM HEPES.NAOH PH 8.0, 10 MM MGCL2, 5 MM NICL2, 7-9% (W/V) PEG 3350, 4% (V/V) 2,2,2-TRIFLUOROETHANOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9919
DetectorDate: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.73→84.08 Å / Num. obs: 24571 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 74.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.73→42.82 Å / Cor.coef. Fo:Fc: 0.9222 / Cor.coef. Fo:Fc free: 0.8926 / SU R Cruickshank DPI: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.804 / SU Rfree Blow DPI: 0.316 / SU Rfree Cruickshank DPI: 0.317
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=18.
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1256 5.11 %RANDOM
Rwork0.2144 ---
obs0.2162 24564 98.7 %-
Displacement parametersBiso mean: 67.86 Å2
Baniso -1Baniso -2Baniso -3
1--6.4053 Å20 Å20 Å2
2---6.4053 Å20 Å2
3---12.8107 Å2
Refine analyzeLuzzati coordinate error obs: 0.404 Å
Refinement stepCycle: LAST / Resolution: 2.73→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 18 159 5295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027032HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2542SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it5218HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion678SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6167SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.85 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3127 158 5.3 %
Rwork0.2465 2823 -
all0.2499 2981 -
obs--98.7 %

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