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- PDB-3vu7: Crystal structure of REV1-REV7-REV3 ternary complex -

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Basic information

Entry
Database: PDB / ID: 3vu7
TitleCrystal structure of REV1-REV7-REV3 ternary complex
Components
  • DNA polymerase zeta catalytic subunit
  • DNA repair protein REV1
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsREPLICATION / DNA polymerase / DNA replication / Translesion DNA synthesis / DNA damage tolerance / DNA repair
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / error-free translesion synthesis ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / error-free translesion synthesis / negative regulation of ubiquitin protein ligase activity / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / telomere maintenance in response to DNA damage / positive regulation of peptidyl-serine phosphorylation / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / response to UV / actin filament organization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of cell growth / Termination of translesion DNA synthesis / negative regulation of canonical Wnt signaling pathway / double-strand break repair via homologous recombination / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transcription corepressor activity / double-strand break repair / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase activity / DNA replication / cell division / nucleotide binding / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
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 / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal ...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 / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / DNA repair protein Rev1 / C4-type zinc-finger of DNA polymerase delta / : / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta catalytic subunit-like, N-terminal domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / BRCA1 C Terminus (BRCT) domain / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase zeta catalytic subunit / DNA repair protein REV1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKikuchi, S. / Hara, K. / Shimizu, T. / Sato, M. / Hashimoto, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis of recruitment of DNA polymerase [zeta] by interaction between REV1 and REV7 proteins
Authors: Kikuchi, S. / Hara, K. / Shimizu, T. / Sato, M. / Hashimoto, H.
History
DepositionJun 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Nov 8, 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
H: DNA repair protein REV1
C: Mitotic spindle assembly checkpoint protein MAD2B
Z: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)45,8293
Polymers45,8293
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-20 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.070, 75.070, 123.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA repair protein REV1 / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 14095.096 Da / Num. of mol.: 1 / Fragment: UNP residues 1140-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2 / REV7 homolog / hREV7


Mass: 26101.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI95
#3: Protein DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / REV3-like / hREV3


Mass: 5632.319 Da / Num. of mol.: 1 / Fragment: UNP residues 1847-1898 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Production host: Escherichia coli (E. coli) / References: UniProt: O60673, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.8 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorDate: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→65.01 Å / Num. obs: 10306

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABD

3abd


Resolution: 2.8→65.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 31.343 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23853 493 4.8 %RANDOM
Rwork0.18888 ---
obs0.19132 9795 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.143 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å2-1.56 Å20 Å2
2---3.11 Å20 Å2
3---4.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 0 0 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9733479
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8695307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59225.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93415479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3881511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211866
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 28 -
Rwork0.401 640 -
obs--100 %
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)
11.53630.10490.29172.3721-0.85611.00740.13830.2244-0.0965-0.09410.01330.01950.00330.1024-0.15160.4096-0.09680.10130.4788-0.03570.436-16.142713.19847.4649
220.2915-12.0841-4.59810.6329-0.08783.3787-0.7140.36881.8133-0.81051.0086-1.11431.232-1.0199-0.29450.6735-0.43630.11590.61840.15650.3956-14.474524.68111.0171
32.390.49110.6293.2024-0.19410.2364-0.13220.0656-0.3779-0.10830.1358-0.2651-0.0816-0.0099-0.00370.4774-0.01280.07780.3799-0.19560.5095-24.5464-13.1457-2.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C10 - 208
2X-RAY DIFFRACTION2Z1873 - 1893
3X-RAY DIFFRACTION3H1157 - 1250

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