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- PDB-6ekl: Crystal structure of mammalian Rev7 in complex with human Chromos... -

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Basic information

Entry
Database: PDB / ID: 6ekl
TitleCrystal structure of mammalian Rev7 in complex with human Chromosome alignment-maintaining phosphoprotein 1
Components
  • Chromosome alignment-maintaining phosphoprotein 1
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsREPLICATION / Rev7 / Mad2L2 / DNA replication / Chromosome Alignment Maintaining Phosphoprotein 1 / Champ1
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 / sister chromatid biorientation / protein localization to microtubule / anaphase-promoting complex / positive regulation of isotype switching ...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 / sister chromatid biorientation / protein localization to microtubule / 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 / attachment of mitotic spindle microtubules to kinetochore / JUN kinase binding / protein localization to kinetochore / 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 / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / condensed chromosome / actin filament organization / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / kinetochore / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / cell division / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Chromosome alignment-maintaining phosphoprotein 1 / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Chromosome alignment-maintaining phosphoprotein 1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 Champ1
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: Chromosome alignment-maintaining phosphoprotein 1


Theoretical massNumber of molelcules
Total (without water)27,4082
Polymers27,4082
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.280, 51.840, 126.180
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(DE3) (bacteria) / References: UniProt: Q9D752
#2: Protein/peptide Chromosome alignment-maintaining phosphoprotein 1 / Zinc finger protein 828


Mass: 2934.389 Da / Num. of mol.: 1 / Fragment: UNP residues 328-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHAMP1, C13orf8, CAMP, CHAMP, KIAA1802, ZNF828 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96JM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M ammonium sulfate, 0.1 M Tris-Bicine pH 8.5, 0.15 M lithium sulfate, 0.02 M sodium nitrate, 0.02 M sodium phosphate dibasic, 1.5% v/v MPD, 1.5% PEG 1000, 1.5% 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: 1.6→70 Å / Num. obs: 41402 / % possible obs: 99.2 % / Redundancy: 8.9 % / Rsym value: 0.101 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 5971 / % possible all: 99.2

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Processing

Software
NameClassification
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8K

5o8k


Resolution: 1.6→23.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2408 -5 %
Rwork0.233 --
obs-41348 99.2 %
Refinement stepCycle: LAST / Resolution: 1.6→23.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 0 33 1835

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