[English] 日本語
Yorodumi
- PDB-2wd5: SMC hinge heterodimer (Mouse) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wd5
TitleSMC hinge heterodimer (Mouse)
Components
  • STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1A
  • STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3
KeywordsCELL CYCLE / DNA DAMAGE / CELL DIVISION
Function / homology
Function and homology information


Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / response to DNA damage checkpoint signaling / SUMOylation of DNA damage response and repair proteins / cohesin loader activity / meiotic cohesin complex / mitotic cohesin complex / cohesin complex / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids ...Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / response to DNA damage checkpoint signaling / SUMOylation of DNA damage response and repair proteins / cohesin loader activity / meiotic cohesin complex / mitotic cohesin complex / cohesin complex / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / synaptonemal complex / lateral element / mediator complex binding / sister chromatid cohesion / mitotic sister chromatid cohesion / dynein complex binding / stem cell population maintenance / beta-tubulin binding / mitotic spindle pole / somatic stem cell population maintenance / regulation of DNA replication / chromosome, centromeric region / basement membrane / mitotic spindle assembly / meiotic cell cycle / response to radiation / kinetochore / nuclear matrix / double-stranded DNA binding / protein heterodimerization activity / cell division / DNA repair / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Smc1, ATP-binding cassette domain / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1A / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMichie, K.A. / Haering, C.H. / Nasmyth, K. / Lowe, J.
CitationJournal: Embo J. / Year: 2011
Title: A Positively Charged Channel within the Smc1/Smc3 Hinge Required for Sister Chromatid Cohesion.
Authors: Kurze, A. / Michie, K.A. / Dixon, S.E. / Mishra, A. / Itoh, T. / Khalid, S. / Strmecki, L. / Shirahige, K. / Haering, C.H. / Lowe, J. / Nasmyth, K.
History
DepositionMar 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1A
B: STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)51,1682
Polymers51,1682
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-6 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.285, 61.867, 77.046
Angle α, β, γ (deg.)90.00, 105.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1A / SMC1ALPHA PROTEIN / CHROMOSOME SEGREGATION PROTEIN SMCB / SB1.8 / SMC1


Mass: 26827.814 Da / Num. of mol.: 1 / Fragment: HINGE DOMAIN, RESIDUES 461-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9CU62
#2: Protein STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 / CHONDROITIN SULFATE PROTEOGLYCAN 6 / CHROMOSOME SEGREGATION PROTEIN SMCD / BASEMENT MEMBRANE- ...CHONDROITIN SULFATE PROTEOGLYCAN 6 / CHROMOSOME SEGREGATION PROTEIN SMCD / BASEMENT MEMBRANE-ASSOCIATED CHONDROITIN PROTEOGLYCAN / MAD MEMBER-INTERACTING PROTEIN 1 / BAMACAN / SMC3


Mass: 24339.887 Da / Num. of mol.: 1 / Fragment: HINGE DOMAIN, RESIDUES 484-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9CW03
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→26 Å / Num. obs: 10243 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 43.59 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→26.05 Å / SU ML: 0.8 / σ(F): 1.28 / Phase error: 36.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.305 1068 5.1 %
Rwork0.225 --
obs0.229 21105 82.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.81 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.0981 Å20 Å211.7286 Å2
2---14.4758 Å20 Å2
3---24.5739 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 0 88 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072978
X-RAY DIFFRACTIONf_angle_d1.0234004
X-RAY DIFFRACTIONf_dihedral_angle_d19.041133
X-RAY DIFFRACTIONf_chiral_restr0.067445
X-RAY DIFFRACTIONf_plane_restr0.004517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.82280.43981150.34572460X-RAY DIFFRACTION81
2.8228-2.97150.38571210.30442503X-RAY DIFFRACTION82
2.9715-3.15730.37711170.27312475X-RAY DIFFRACTION82
3.1573-3.40060.30341160.23942532X-RAY DIFFRACTION82
3.4006-3.7420.31911740.19752511X-RAY DIFFRACTION84
3.742-4.28140.26241500.18632513X-RAY DIFFRACTION83
4.2814-5.38620.27091480.17062500X-RAY DIFFRACTION83
5.3862-26.05490.26391270.21092543X-RAY DIFFRACTION84

+
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