[English] 日本語
Yorodumi
- PDB-4je3: An Iml3-Chl4 heterodimer links the core centromere to factors req... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4je3
TitleAn Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation
Components
  • Central kinetochore subunit CHL4
  • Central kinetochore subunit IML3
KeywordsCELL CYCLE / kinetochore / beta sheet / chromosome segregation / Iml3-Chl4 dimer / nucleus
Function / homology
Function and homology information


maintenance of meiotic sister chromatid cohesion / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly ...maintenance of meiotic sister chromatid cohesion / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / mitotic spindle assembly checkpoint signaling / meiotic cell cycle / chromosome segregation / kinetochore / cell division / structural molecule activity / nucleus
Similarity search - Function
Ubiquitin-like (UB roll) - #720 / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Inner kinetochore subunit IML3 / Inner kinetochore subunit CHL4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsHinshaw, S.M. / Harrison, S.C.
CitationJournal: Cell Rep / Year: 2013
Title: An iml3-chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation.
Authors: Hinshaw, S.M. / Harrison, S.C.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Central kinetochore subunit IML3
B: Central kinetochore subunit CHL4


Theoretical massNumber of molelcules
Total (without water)39,0902
Polymers39,0902
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-9 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.483, 143.916, 146.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Central kinetochore subunit IML3 / Increased minichromosome loss protein 3 / Minichromosome maintenance protein 19


Mass: 28048.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IML3, MCM19, YBR107C, YBR0836 / Production host: Escherichia coli (E. coli) / References: UniProt: P38265
#2: Protein Central kinetochore subunit CHL4 / Chromosome loss protein 4 / Chromosome transmission fidelity protein 17 / Minichromosome ...Chromosome loss protein 4 / Chromosome transmission fidelity protein 17 / Minichromosome maintenance protein 17


Mass: 11041.485 Da / Num. of mol.: 1 / Fragment: UNP residues 361-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHL4, CTF17, MCM17, YDR254W, YD9320A.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P38907
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.35 M lithium citrate, pH 9, 25% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2012
RadiationMonochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.282→50 Å / Num. obs: 19061 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Χ2: 0.94 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.282-2.376.20.45317130.673191.4
2.37-2.477.20.39118860.715198.8
2.47-2.587.20.31318990.792199.3
2.58-2.727.30.23118730.9641100
2.72-2.897.30.1619021.079199.6
2.89-3.117.30.11719041.068199.7
3.11-3.427.30.08519091.076199.8
3.42-3.927.20.06519440.949199.8
3.92-4.936.90.05719631.0141100
4.93-506.60.04520681.0021100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.282→36 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2106 1866 10 PERCENT IN EACH SHELL
Rwork0.1827 --
obs0.1855 18652 -
Displacement parametersBiso max: 143.24 Å2 / Biso mean: 47.7329 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: LAST / Resolution: 2.282→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 0 136 2701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.175
X-RAY DIFFRACTIONf_chiral_restr0.066
X-RAY DIFFRACTIONf_plane_restr0.006
X-RAY DIFFRACTIONf_dihedral_angle_d15.13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.282-2.34380.27491300.2405X-RAY DIFFRACTION91
2.3438-2.41280.26831380.2131X-RAY DIFFRACTION93
2.4128-2.49060.25991390.2156X-RAY DIFFRACTION96
2.4906-2.57960.24051390.2101X-RAY DIFFRACTION96
2.5796-2.68290.261390.2039X-RAY DIFFRACTION97
2.6829-2.80490.24661430.2102X-RAY DIFFRACTION98
2.8049-2.95270.2261490.1968X-RAY DIFFRACTION99
2.9527-3.13760.23471440.2102X-RAY DIFFRACTION99
3.1376-3.37970.20751410.1964X-RAY DIFFRACTION99
3.3797-3.71950.20191430.1654X-RAY DIFFRACTION100
3.7195-4.2570.17681470.1576X-RAY DIFFRACTION100
4.257-5.36050.16991530.1467X-RAY DIFFRACTION100
5.3605-35.98350.21481610.1967X-RAY DIFFRACTION99

+
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