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- PDB-6ekm: Crystal structure of mammalian Rev7 in complex with human Rev3 se... -

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Basic information

Entry
Database: PDB / ID: 6ekm
TitleCrystal structure of mammalian Rev7 in complex with human Rev3 second binding site
Components
  • DNA polymerase zeta catalytic subunit
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsREPLICATION / Rev7 / Mad2L2 / DNA replication / Rev3 / DNA polymerase zeta
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 / telomere maintenance in response to DNA damage / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly ...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 / telomere maintenance in response to DNA damage / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / 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 / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of cell growth / actin filament organization / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell cycle / cell division / nucleotide binding / positive regulation of gene expression / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily ...Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional 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 / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsHuber, F. / Tropia, L. / Emamzadah, S. / 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 human Rev3
Authors: Huber, F. / Tropia, L. / Emamzadah, S. / Halazonetis, T.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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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)27,6792
Polymers27,6792
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-23 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.200, 48.640, 116.810
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 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 BL21 (bacteria) / References: UniProt: Q9D752
#2: Protein/peptide DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / hREV3


Mass: 3205.942 Da / Num. of mol.: 1 / Fragment: UNP residues 1989-2014
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O60673, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium formate, 0.1 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate, 0.1 M sodium potassium tartrate tetrahydrate, 0.1 M sodium oxamate, 0.1 M Imidazole - MES monohydrate ...Details: 0.1 M sodium formate, 0.1 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate, 0.1 M sodium potassium tartrate tetrahydrate, 0.1 M sodium oxamate, 0.1 M Imidazole - MES monohydrate (acid) pH 6.5 and 12.5% v/v MPD, 12.5% PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.76→58.4 Å / Num. obs: 5897 / % possible obs: 99.7 % / Redundancy: 5.45 % / Rsym value: 0.182 / Net I/σ(I): 7.5
Reflection shellResolution: 2.76→2.95 Å / Redundancy: 5.14 % / Num. unique obs: 4231 / Rsym value: 0.415 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EKL

6ekl


Resolution: 2.76→58.4 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25843 298 4.9 %RANDOM
Rwork0.23009 ---
obs0.23152 5820 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.843 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å2-0 Å20 Å2
2--5.43 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.76→58.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 0 21 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191856
X-RAY DIFFRACTIONr_bond_other_d00.021877
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9762518
X-RAY DIFFRACTIONr_angle_other_deg3.35234329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2025222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.24424.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.538159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02387
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_it1.9315.603894
X-RAY DIFFRACTIONr_mcbond_other1.9325.599893
X-RAY DIFFRACTIONr_mcangle_it3.338.391114
X-RAY DIFFRACTIONr_mcangle_other3.3288.3951115
X-RAY DIFFRACTIONr_scbond_it2.4915.717962
X-RAY DIFFRACTIONr_scbond_other2.4915.717962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7528.4771404
X-RAY DIFFRACTIONr_long_range_B_refined6.84643.3462092
X-RAY DIFFRACTIONr_long_range_B_other6.84443.3692093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 30 -
Rwork0.337 408 -
obs--99.55 %

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