[English] 日本語
Yorodumi
- PDB-5xpu: Crystal structure of MAD2L2/REV7 in complex with a CAMP fragment ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xpu
TitleCrystal structure of MAD2L2/REV7 in complex with a CAMP fragment in a monoclinic 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 / zeta DNA polymerase complex / sister chromatid biorientation / protein localization to microtubule / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / attachment of mitotic spindle microtubules to kinetochore / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding ...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 / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / attachment of mitotic spindle microtubules to kinetochore / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / protein localization to kinetochore / negative regulation of epithelial to mesenchymal transition / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / negative regulation of ubiquitin protein ligase activity / 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 / condensed chromosome / 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 / negative regulation of protein catabolic process / kinetochore / spindle / transcription corepressor activity / double-strand break repair / 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 / zinc ion binding / nucleoplasm / nucleus / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 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 1.2Dec 25, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.3Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein is a monomer in solution by the gel filtration analysis, but it clearly forms a dimer in crystal.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.025, 70.562, 45.131
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe authors state that MAD2L2-CAMP complex forms hetero tetrameric composed of two MAD2L2, and two CAMP

-
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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M potassium thiocyanate, 20% PEG 3350

-
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 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→19.09 Å / Num. obs: 9883 / % possible obs: 99.6 % / Redundancy: 3.4 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.43 Å

-
Processing

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

3abe


Resolution: 2.304→19.09 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2273 479 4.85 %
Rwork0.2199 --
obs0.2202 9876 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→19.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 0 32 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011574
X-RAY DIFFRACTIONf_angle_d1.2692141
X-RAY DIFFRACTIONf_dihedral_angle_d16.648586
X-RAY DIFFRACTIONf_chiral_restr0.047255
X-RAY DIFFRACTIONf_plane_restr0.007268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.63660.28411610.27583107X-RAY DIFFRACTION99
2.6366-3.3190.29781730.25023110X-RAY DIFFRACTION100
3.319-19.09050.1841450.19673180X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more