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- PDB-5o8k: Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895 -

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Basic information

Entry
Database: PDB / ID: 5o8k
TitleCrystal structure of mammalian Rev7 in complex with Rev3 1875-1895
Components
  • DNA polymerase zeta catalytic subunit
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsREPLICATION / Rev7 / Mad2L2 / DNA Polymerase zeta / DNA replication
Function / homology
Function and homology information


Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin ...Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / zeta DNA polymerase complex / anaphase-promoting 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 / negative regulation of ubiquitin protein ligase activity / positive regulation of double-strand break repair via nonhomologous end joining / 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 / actin filament organization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of cell growth / 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 / double-strand break repair / site of double-strand break / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase activity / 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 / nucleus / cytoplasm
Similarity search - Function
Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / 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 ...Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / 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 / 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 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase zeta catalytic subunit / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsEmamzadah, S. / Tropia, L. / Huber, F. / Halazonetis, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation160322 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895
Authors: Emamzadah, S. / Tropia, L. / Huber, F. / Halazonetis, T.
History
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Mitotic spindle assembly checkpoint protein MAD2B
B: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)27,6152
Polymers27,6152
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.014, 69.014, 42.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2


Mass: 24473.545 Da / Num. of mol.: 1 / Mutation: F11S, G12A, V132K, C133V, A135K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mad2l2, Mad2b, Rev7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q9D752
#2: Protein/peptide DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / hREV3


Mass: 3141.685 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60673, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 2000 MME, 0.8M sodium formate, 0.1M tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9334 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→70 Å / Num. obs: 20408 / % possible obs: 96.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.071 / Rrim(I) all: 0.139 / Net I/σ(I): 7.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3080 / Rpim(I) all: 0.166 / Rrim(I) all: 0.362 / % possible all: 99.6

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Processing

Software
NameClassification
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementStarting model: 3ABD

3abd


Resolution: 1.8→70 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2888 --
Rwork0.2552 --
obs-20408 96.4 %
Refinement stepCycle: LAST / Resolution: 1.8→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 0 37 1853

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