[English] 日本語
Yorodumi
- PDB-2yfv: The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfv
TitleThe heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4
Components
  • HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
  • HISTONE H4
  • SCM3
KeywordsCELL CYCLE / KINETOCHORE / CENTROMERE / HISTONE CHAPERONE / BUDDING YEAST
Function / homology
Function and homology information


CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / protein localization to chromosome, centromeric region / kinetochore assembly / CENP-A containing nucleosome / negative regulation of ubiquitin-dependent protein catabolic process / chromosome segregation / structural constituent of chromatin / G2/M transition of mitotic cell cycle / histone binding ...CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / protein localization to chromosome, centromeric region / kinetochore assembly / CENP-A containing nucleosome / negative regulation of ubiquitin-dependent protein catabolic process / chromosome segregation / structural constituent of chromatin / G2/M transition of mitotic cell cycle / histone binding / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2010 / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2010 / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helix non-globular / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Special / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / KLLA0F05115p / 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: 2.32 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
B: HISTONE H4
C: SCM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8345
Polymers27,5803
Non-polymers2542
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-57.7 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.723, 65.530, 121.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 11692.733 Da / Num. of mol.: 1 / Fragment: RESIDUES 81-180
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: 8456.876 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-98
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: Protein SCM3 / KLLA0F05115P


Mass: 7430.433 Da / Num. of mol.: 1 / Fragment: RESIDUES 41-103
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: Q6CL77
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 4.5
Details: 0.1 M SODIUM CITRATE, PH4.5, 6% PEG 4000, AND 0.1 M SODIUM IODIDE

-
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: Oct 10, 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: 2.3→50 Å / Num. obs: 11636 / % possible obs: 94.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.5 / % possible all: 55.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQZ

1eqz


Resolution: 2.32→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.225 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 126-130 OF CHAIN A ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25712 555 4.8 %RANDOM
Rwork0.22026 ---
obs0.22195 11073 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.054 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2--3.52 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 2 58 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9692215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27522.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.35915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8051520
X-RAY DIFFRACTIONr_chiral_restr0.1060.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021177
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_it0.6731.51001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35621620
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4093651
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1634.5595
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: 2.322→2.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 35 -
Rwork0.293 656 -
obs--81.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3373-0.11912.62121.4610.47716.1363-0.07330.33550.102-0.254-0.04920.0637-0.172-0.12070.12250.03730.00220.02450.05530.05630.0982-10.619710.3622-29.0981
22.1331-0.3032-1.09012.37961.9710.41280.03490.4277-0.0208-0.59940.0127-0.0813-0.386-0.2845-0.04760.0457-0.0295-0.00830.05050.04720.0984-12.26819.9319-33.9279
31.02991.28431.7021.08931.36391.2329-0.15730.0928-0.1224-0.16530.10490.0266-0.19530.08320.05240.1369-0.01390.01540.2077-0.00410.1968-4.2359-4.0081-27.0598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 120
2X-RAY DIFFRACTION1A121 - 133
3X-RAY DIFFRACTION1A134 - 168
4X-RAY DIFFRACTION1A169 - 176
5X-RAY DIFFRACTION1A177 - 180
6X-RAY DIFFRACTION2B24 - 34
7X-RAY DIFFRACTION2B35 - 40
8X-RAY DIFFRACTION2B41 - 66
9X-RAY DIFFRACTION2B67 - 78
10X-RAY DIFFRACTION2B79 - 95
11X-RAY DIFFRACTION3C44 - 57
12X-RAY DIFFRACTION3C58 - 68
13X-RAY DIFFRACTION3C69 - 76
14X-RAY DIFFRACTION3C77 - 90
15X-RAY DIFFRACTION3C91 - 104

+
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