[English] 日本語
Yorodumi
- PDB-6s29: Structure of fission yeast Mis16-Mis19 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s29
TitleStructure of fission yeast Mis16-Mis19 complex
Components
  • CENP-A recruiting complex protein mis19
  • Histone acetyltransferase type B subunit 2
KeywordsCELL CYCLE / centromere mitosis WD40 histone chaperone
Function / homology
Function and homology information


HATs acetylate histones / RMTs methylate histone arginines / Neddylation / HDACs deacetylate histones / CENP-A recruiting complex / chromosome, centromeric core domain / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore ...HATs acetylate histones / RMTs methylate histone arginines / Neddylation / HDACs deacetylate histones / CENP-A recruiting complex / chromosome, centromeric core domain / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / kinetochore / histone binding / chromatin remodeling / cell division / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
EIPR1 beta-propeller / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...EIPR1 beta-propeller / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / CENP-A recruiting complex protein mis19 / Histone acetyltransferase type B subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsLefevre, S. / Korntner-Vetter, M. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
Cancer Research UKFC001155 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2019
Title: Subunit interactions and arrangements in the fission yeast Mis16-Mis18-Mis19 complex.
Authors: Korntner-Vetter, M. / Lefevre, S. / Hu, X.W. / George, R. / Singleton, M.R.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Histone acetyltransferase type B subunit 2
B: CENP-A recruiting complex protein mis19
C: Histone acetyltransferase type B subunit 2
D: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,96610
Polymers111,4864
Non-polymers4796
Water13,980776
1
A: Histone acetyltransferase type B subunit 2
B: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9835
Polymers55,7432
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area21300 Å2
MethodPISA
2
C: Histone acetyltransferase type B subunit 2
D: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9835
Polymers55,7432
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-6 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.171, 99.035, 109.880
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Histone acetyltransferase type B subunit 2 / Kinetochore protein mis16


Mass: 48407.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mis16, hat2, SPCC1672.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94244
#2: Protein CENP-A recruiting complex protein mis19 / Eighteen-interacting centromere protein 1 / Kinetochore protein mis19


Mass: 7335.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mis19, eic1, kis1, SPBC27B12.02, SPBC30B4.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O42995
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.6 M NaBr, 0.1 M Tris pH 9.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.988→54.28 Å / Num. obs: 69320 / % possible obs: 89.56 % / Redundancy: 5.6 % / Net I/σ(I): 8.11
Reflection shellResolution: 1.988→2.06 Å / Num. unique obs: 3761

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1L

6s1l


Resolution: 1.988→54.28 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.96
RfactorNum. reflection% reflection
Rfree0.2342 3556 5.14 %
Rwork0.1959 --
obs0.1979 69227 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.988→54.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 6 776 7945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097337
X-RAY DIFFRACTIONf_angle_d1.1069992
X-RAY DIFFRACTIONf_dihedral_angle_d7.2474383
X-RAY DIFFRACTIONf_chiral_restr0.0661108
X-RAY DIFFRACTIONf_plane_restr0.0071303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9879-2.01510.3096660.28061224X-RAY DIFFRACTION42
2.0151-2.04390.3256860.2581507X-RAY DIFFRACTION51
2.0439-2.07440.3279880.26341637X-RAY DIFFRACTION57
2.0744-2.10680.2992980.25461854X-RAY DIFFRACTION63
2.1068-2.14130.27311140.24142023X-RAY DIFFRACTION70
2.1413-2.17830.2921370.24442168X-RAY DIFFRACTION75
2.1783-2.21790.26451340.23462461X-RAY DIFFRACTION84
2.2179-2.26050.29481470.22642815X-RAY DIFFRACTION97
2.2605-2.30670.281720.22622937X-RAY DIFFRACTION100
2.3067-2.35680.27721730.23372873X-RAY DIFFRACTION100
2.3568-2.41170.27411480.22832959X-RAY DIFFRACTION100
2.4117-2.4720.29431860.22462878X-RAY DIFFRACTION100
2.472-2.53880.28111620.21732945X-RAY DIFFRACTION100
2.5388-2.61350.27541530.21592918X-RAY DIFFRACTION100
2.6135-2.69790.27741640.20272927X-RAY DIFFRACTION100
2.6979-2.79430.24571530.2052957X-RAY DIFFRACTION100
2.7943-2.90620.2381270.20762929X-RAY DIFFRACTION100
2.9062-3.03840.24821550.2092928X-RAY DIFFRACTION100
3.0384-3.19860.2321520.20252959X-RAY DIFFRACTION100
3.1986-3.3990.23951570.18922925X-RAY DIFFRACTION100
3.399-3.66140.1951670.16872932X-RAY DIFFRACTION100
3.6614-4.02970.2051550.16652970X-RAY DIFFRACTION100
4.0297-4.61250.19311500.15132944X-RAY DIFFRACTION100
4.6125-5.81030.17141660.16372976X-RAY DIFFRACTION100
5.8103-54.30370.20631460.20083025X-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