[English] 日本語
Yorodumi
- PDB-7x85: Crystal structure of chicken CENP-C Cupin domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x85
TitleCrystal structure of chicken CENP-C Cupin domain
ComponentsCENP-C
KeywordsCELL CYCLE / Kinetochore / Centromere / Chromosome segregation / dimerization
Function / homology
Function and homology information


centromeric DNA binding / kinetochore assembly / kinetochore / nucleus
Similarity search - Function
Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
CITRIC ACID / CENP-C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.639 Å
AuthorsAriyoshi, M. / Hara, M. / Fukagawa, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06084 Japan
CitationJournal: Mol.Cell / Year: 2023
Title: Centromere/kinetochore is assembled through CENP-C oligomerization.
Authors: Hara, M. / Ariyoshi, M. / Sano, T. / Nozawa, R.S. / Shinkai, S. / Onami, S. / Jansen, I. / Hirota, T. / Fukagawa, T.
History
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CENP-C
B: CENP-C
C: CENP-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,66511
Polymers63,6283
Non-polymers1,0378
Water18010
1
A: CENP-C
B: CENP-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8955
Polymers42,4192
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-32 kcal/mol
Surface area12370 Å2
MethodPISA
2
C: CENP-C
hetero molecules

C: CENP-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,54012
Polymers42,4192
Non-polymers1,12110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7310 Å2
ΔGint-29 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.587, 112.587, 212.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein CENP-C


Mass: 21209.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: O57393
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.12 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M lithium citrate, 0.1 M MES-NaOH pH 6.5 and 20% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.639→48.75 Å / Num. obs: 24156 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.036 / Rrim(I) all: 0.118 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.75-48.7514.90.0257900.9990.0090.027
2.64-2.7719.92.82130930.7350.9022.963

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPV

2vpv


Resolution: 2.639→47.558 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.945 / SU B: 24.883 / SU ML: 0.217 / Cross valid method: FREE R-VALUE / ESU R Free: 0.25 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2517 1170 4.858 %
Rwork0.185 22916 -
all0.188 --
obs-24086 99.76 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 97.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.075 Å20.037 Å20 Å2
2--0.075 Å2-0 Å2
3----0.243 Å2
Refinement stepCycle: LAST / Resolution: 2.639→47.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 69 10 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123176
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.634299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92424.452146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.646156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022363
X-RAY DIFFRACTIONr_nbd_refined0.220.21081
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2109
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.26
X-RAY DIFFRACTIONr_mcbond_it6.2915.7181537
X-RAY DIFFRACTIONr_mcangle_it8.3388.5791916
X-RAY DIFFRACTIONr_scbond_it8.4066.1971639
X-RAY DIFFRACTIONr_scangle_it10.1119.1152383
X-RAY DIFFRACTIONr_lrange_it10.80276.4994228
X-RAY DIFFRACTIONr_rigid_bond_restr2.91933176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.639-2.7070.39810.3491633X-RAY DIFFRACTION98.3362
2.707-2.7820.378870.3131595X-RAY DIFFRACTION99.7627
2.782-2.8620.287640.2621597X-RAY DIFFRACTION99.9398
2.862-2.950.316830.2321533X-RAY DIFFRACTION99.9382
2.95-3.0470.261660.2221496X-RAY DIFFRACTION99.8721
3.047-3.1540.255720.1951431X-RAY DIFFRACTION99.8008
3.154-3.2730.229720.1881381X-RAY DIFFRACTION100
3.273-3.4070.179600.1611355X-RAY DIFFRACTION100
3.407-3.5580.221620.1771307X-RAY DIFFRACTION99.927
3.558-3.7320.264570.1721238X-RAY DIFFRACTION99.8458
3.732-3.9330.208690.171173X-RAY DIFFRACTION100
3.933-4.1720.253600.1541129X-RAY DIFFRACTION100
4.172-4.460.184590.1371056X-RAY DIFFRACTION99.9104
4.46-4.8170.193580.128986X-RAY DIFFRACTION100
4.817-5.2760.155400.124924X-RAY DIFFRACTION100
5.276-5.8990.248420.148853X-RAY DIFFRACTION100
5.899-6.810.3510.208740X-RAY DIFFRACTION100
6.81-8.3390.274450.247644X-RAY DIFFRACTION100
8.339-11.7840.342220.19530X-RAY DIFFRACTION99.639
11.784-47.5580.476200.288315X-RAY DIFFRACTION96.5418
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)
12.5328-0.67931.24274.7454-1.59313.7905-0.2494-0.30280.38050.29720.33160.3584-0.8293-0.6444-0.08220.65080.48570.03110.3881-0.030.2043-39.658234.3336.9734
22.74370.3163-0.17144.0631-0.95452.8914-0.24410.39260.0913-0.18690.32840.2987-0.6461-0.6143-0.08430.50460.3308-0.05330.4717-0.03260.1802-40.1431.2354-6.5424
32.3933-0.4475-0.59024.52711.41314.1118-0.2533-0.3339-0.18520.42560.4712-0.39180.11840.1863-0.21790.11410.0943-0.02630.0947-0.0180.0632-15.9519-1.48936.7133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA723 - 849
2X-RAY DIFFRACTION2ALLB721 - 850
3X-RAY DIFFRACTION3ALLC722 - 849

+
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