[English] 日本語
Yorodumi
- PDB-2yfw: Heterotetramer structure of Kluyveromyces lactis Cse4,H4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfw
TitleHeterotetramer structure of Kluyveromyces lactis Cse4,H4
Components
  • HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
  • HISTONE H4
KeywordsCELL CYCLE / KINETOCHORE / CENTROMERE / HISTONE CHAPERONE / BUDDING YEAST
Function / homology
Function and homology information


protein localization to CENP-A containing chromatin / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / CENP-A containing nucleosome / centromeric DNA binding / kinetochore assembly / mitotic sister chromatid segregation / kinetochore / nucleosome / protein heterodimerization activity ...protein localization to CENP-A containing chromatin / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / CENP-A containing nucleosome / centromeric DNA binding / kinetochore assembly / mitotic sister chromatid segregation / kinetochore / nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 ...Histone, subunit A / Histone, subunit A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone H3-like centromeric protein CSE4
Similarity search - Component
Biological speciesKLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, U.S. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Recognition of the Centromere-Specific Histone Cse4 by the Chaperone Scm3.
Authors: Cho, U.S. / Harrison, S.C.
History
DepositionApr 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
B: HISTONE H4
C: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
D: HISTONE H4
E: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
F: HISTONE H4
G: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
H: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)88,7328
Polymers88,7328
Non-polymers00
Water25214
1
A: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
B: HISTONE H4
G: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
H: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)44,3664
Polymers44,3664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-99.4 kcal/mol
Surface area15490 Å2
MethodPISA
2
C: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
D: HISTONE H4
E: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
F: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)44,3664
Polymers44,3664
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-93.9 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)169.479, 169.479, 81.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9234, 0.2429, 0.2972), (0.3676, 0.3371, 0.8667), (0.1104, 0.9096, -0.4005)89.73, -27.38, 10.52
2given(-0.9234, 0.2429, 0.2972), (0.3676, 0.3371, 0.8667), (0.1104, 0.9096, -0.4005)89.73, -27.38, 10.52
3given(0.01418, 0.4677, -0.8838), (0.5252, -0.7556, -0.3915), (-0.8509, -0.4586, -0.2563)45.74, -66.56, 17
4given(-0.09929, -0.7736, 0.6258), (-0.5608, -0.476, -0.6775), (0.822, -0.4182, -0.3866)33.38, -17.42, -51.05

-
Components

#1: Protein
HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 / CENP-A HOMOLOG / CHROMOSOME SEGREGATION PROTEIN 4 / CSE4


Mass: 10746.627 Da / Num. of mol.: 4 / Fragment: HISTONE-FOLD DOMAIN, RESIDUES 93-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CTI2
#2: Protein
HISTONE H4 / / H4


Mass: 11436.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CMU6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97914
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010 / Details: MIRRORS
RadiationMonochromator: CHOZU HLD8-24 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26486 / % possible obs: 99.9 % / Observed criterion σ(I): 1.3 / Redundancy: 3.8 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQZ
Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / SU B: 27.088 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 93-104, 128,184 FOR CHAIN A, RESIDUES 1-28,95-103 FOR CHAIN B, RESIDUES 93-103, 123-130, 182-184 FOR CHAIN C, RESIDUES 1-23, 95- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 93-104, 128,184 FOR CHAIN A, RESIDUES 1-28,95-103 FOR CHAIN B, RESIDUES 93-103, 123-130, 182-184 FOR CHAIN C, RESIDUES 1-23, 95-103 FOR CHAIN D, RESIDUES 126-129 FOR CHAIN E, RESIDUES 1-22, 95-103 FOR CHAIN F, RESIDUES 93-103, 182-184 FOR CHAIN G, RESIDUES 1-22,103 FOR CHAIN H ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27633 1342 5 %RANDOM
Rwork0.21828 ---
obs0.22112 25302 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.28 Å20 Å2
2--0.57 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 14 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9736524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98420.927205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.73215951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1061569
X-RAY DIFFRACTIONr_chiral_restr0.1010.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.52990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1124800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94731870
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4654.51724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 98 -
Rwork0.289 1829 -
obs--97.82 %

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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