[English] 日本語
Yorodumi
- PDB-3vh6: Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vh6
TitleCrystal structure of the chicken CENP-T histone fold/CENP-W/CENP-S/CENP-X heterotetrameric complex, crystal form II
Components
  • CENP-S
  • CENP-T
  • CENP-W
  • CENP-X
KeywordsDNA BINDING PROTEIN / histone fold / chromosome segregation / DNA binding / nucleus
Function / homology
Function and homology information


PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RHO GTPases Activate Formins / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / Separation of Sister Chromatids / FANCM-MHF complex / Fanconi anaemia nuclear complex ...PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RHO GTPases Activate Formins / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / Separation of Sister Chromatids / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / chromosome segregation / kinetochore / mitotic cell cycle / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein S / Centromere protein T / Centromere protein W / Centromere protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.351 Å
AuthorsNishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold
Authors: Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.
History
DepositionAug 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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: CENP-S
D: CENP-X
T: CENP-T
W: CENP-W


Theoretical massNumber of molelcules
Total (without water)46,4624
Polymers46,4624
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-94 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.510, 158.510, 158.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein CENP-S


Mass: 15561.421 Da / Num. of mol.: 1 / Mutation: C26A, C28A, C55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: E1BSW7*PLUS
#2: Protein CENP-X


Mass: 9361.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P0DJH7*PLUS
#3: Protein CENP-T


Mass: 12682.790 Da / Num. of mol.: 1 / Fragment: C-terminal histone fold / Mutation: C87A, C161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPT / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: F1NPG5
#4: Protein CENP-W


Mass: 8855.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P0DJH6*PLUS
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR CHAIN A, D, W DO NOT CURRENTLY EXIST. CHAIN A IS C26A, C28A, C55A MUTANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 5.6% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2011
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.35→37.4 Å / Num. all: 9985 / Num. obs: 9626 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 115.15 Å2
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.88 / Num. unique all: 938 / Rsym value: 0.726 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH5

3vh5


Resolution: 3.351→37.361 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7888 / SU ML: 1.09 / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1915 19.92 %random
Rwork0.2111 ---
all0.2237 9626 --
obs0.2237 9615 99.29 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.058 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 352.23 Å2 / Biso mean: 117.7597 Å2 / Biso min: 59.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.351→37.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 0 0 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112797
X-RAY DIFFRACTIONf_angle_d1.3573755
X-RAY DIFFRACTIONf_chiral_restr0.087438
X-RAY DIFFRACTIONf_plane_restr0.005477
X-RAY DIFFRACTIONf_dihedral_angle_d18.3261082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3506-3.43440.39051360.3398539675100
3.4344-3.52720.35451340.2912558692100
3.5272-3.63090.34851380.2786548686100
3.6309-3.7480.31621350.2359541676100
3.748-3.88180.25851360.2017546682100
3.8818-4.0370.28561390.2022553692100
4.037-4.22050.2951300.21285416711.01
4.2205-4.44270.30031410.1883553694100
4.4427-4.72050.2571340.1762556690100
4.7205-5.08420.25751380.1918551689100
5.0842-5.59430.31851350.2389554689100
5.5943-6.40030.32721390.287255769699
6.4003-8.05040.28051400.178255569599
8.0504-37.36350.20171400.185954868894

+
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