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- PDB-5xpt: Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment ... -

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Basic information

Entry
Database: PDB / ID: 5xpt
TitleCrystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a tetragonal crystal
Components
  • Chromosome alignment-maintaining phosphoprotein 1
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsTRANSCRIPTION/METAL BINDING PROTEIN / MAD2L2 / MAD2B / REV7 / CAMP / champ1 / TRANSCRIPTION-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / sister chromatid biorientation / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / protein localization to microtubule / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of epithelial to mesenchymal transition ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / sister chromatid biorientation / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / protein localization to microtubule / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of epithelial to mesenchymal transition / 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 ubiquitin protein ligase activity / negative regulation of double-strand break repair via homologous recombination / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of epithelial to mesenchymal transition / error-prone translesion synthesis / condensed chromosome / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / kinetochore / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / cell division / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Chromosome alignment-maintaining phosphoprotein 1 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / zinc finger / Zinc finger C2H2 type domain profile. ...Chromosome alignment-maintaining phosphoprotein 1 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome alignment-maintaining phosphoprotein 1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsHara, K. / Taharazako, S. / Hashimoto, H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Dynamic feature of mitotic arrest deficient 2-like protein 2 (MAD2L2) and structural basis for its interaction with chromosome alignment-maintaining phosphoprotein (CAMP).
Authors: Hara, K. / Taharazako, S. / Ikeda, M. / Fujita, H. / Mikami, Y. / Kikuchi, S. / Hishiki, A. / Yokoyama, H. / Ishikawa, Y. / Kanno, S.I. / Tanaka, K. / Hashimoto, H.
History
DepositionJun 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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
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: Chromosome alignment-maintaining phosphoprotein 1


Theoretical massNumber of molelcules
Total (without water)28,1872
Polymers28,1872
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-14 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.493, 106.493, 127.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

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Components

#1: 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 / Mutation: R124A
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
#2: Protein/peptide Chromosome alignment-maintaining phosphoprotein 1 / Zinc finger protein 828


Mass: 2085.340 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 325-344
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 (E. coli) / References: UniProt: Q96JM3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M sodium cacodylate pH 6.6, 4.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→19.85 Å / Num. obs: 21579 / % possible obs: 99.8 % / Redundancy: 13.1 % / Net I/σ(I): 27.5
Reflection shellResolution: 2.1→2.22 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABE

3abe


Resolution: 2.102→19.846 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.226 1063 4.93 %
Rwork0.1973 --
obs0.1987 21575 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→19.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 0 120 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091731
X-RAY DIFFRACTIONf_angle_d1.112355
X-RAY DIFFRACTIONf_dihedral_angle_d13.306651
X-RAY DIFFRACTIONf_chiral_restr0.043277
X-RAY DIFFRACTIONf_plane_restr0.005298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1023-2.19780.2811090.23682501X-RAY DIFFRACTION98
2.1978-2.31350.27341340.21642513X-RAY DIFFRACTION100
2.3135-2.45820.2071700.20372499X-RAY DIFFRACTION100
2.4582-2.64760.27131300.22212543X-RAY DIFFRACTION100
2.6476-2.91330.26781250.21992560X-RAY DIFFRACTION100
2.9133-3.33320.27411420.2142561X-RAY DIFFRACTION100
3.3332-4.19290.1761080.17692621X-RAY DIFFRACTION100
4.1929-19.8470.20041450.17912714X-RAY DIFFRACTION100

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