[English] 日本語
Yorodumi
- PDB-7da0: High-resolution crystal structure of the chicken MHF complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7da0
TitleHigh-resolution crystal structure of the chicken MHF complex
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / histone fold / DNA binding / DNA repair / 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 / kinetochore / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding
Similarity search - Function
Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone-fold
Similarity search - Domain/homology
Centromere protein S / Centromere protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsIto, S. / Nishino, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07279 Japan
Japan Society for the Promotion of Science (JSPS)16K07279 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural analysis of the chicken FANCM-MHF complex and its stability.
Authors: Ito, S. / Nishino, T.
History
DepositionOct 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Centromere protein S
C: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)21,2372
Polymers21,2372
Non-polymers00
Water4,486249
1
B: Centromere protein S
C: Centromere protein X

B: Centromere protein S
C: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)42,4744
Polymers42,4744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11190 Å2
ΔGint-96 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.566, 69.071, 48.878
Angle α, β, γ (deg.)90.000, 103.666, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-256-

HOH

21C-197-

HOH

-
Components

#1: Protein Centromere protein S / CENP-S


Mass: 11875.330 Da / Num. of mol.: 1 / Mutation: C26A, C28A, C55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPS, APITD1 / Plasmid: pRSFDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1BSW7
#2: Protein Centromere protein X / CENP-X


Mass: 9361.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPX, STRA13 / Plasmid: pRSFDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DJH7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-Bicine pH 8.5, 0.1 M Carboxylic acids mix, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→34.01 Å / Num. obs: 43638 / % possible obs: 96.74 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.0056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Net I/σ(I): 36.64
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4340 / Rpim(I) all: 0.52 / Rrim(I) all: 0.999 / % possible all: 96.21

-
Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0B

3b0b


Resolution: 1.25→34.01 Å / SU ML: 0.1362 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 2000 4.58 %
Rwork0.1927 41628 -
obs0.1936 43628 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.88 Å2
Refinement stepCycle: LAST / Resolution: 1.25→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 0 249 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881371
X-RAY DIFFRACTIONf_angle_d0.97451840
X-RAY DIFFRACTIONf_chiral_restr0.0675216
X-RAY DIFFRACTIONf_plane_restr0.0054238
X-RAY DIFFRACTIONf_dihedral_angle_d19.1906526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.29711430.30092968X-RAY DIFFRACTION95.55
1.28-1.320.28991420.28092955X-RAY DIFFRACTION97.94
1.32-1.350.26031430.25252997X-RAY DIFFRACTION98.19
1.35-1.40.2641460.24323029X-RAY DIFFRACTION98.45
1.4-1.450.25781440.23143011X-RAY DIFFRACTION98.44
1.45-1.510.23311460.20983017X-RAY DIFFRACTION98.57
1.51-1.570.23231470.1933045X-RAY DIFFRACTION98.4
1.58-1.660.22491430.18352992X-RAY DIFFRACTION98.55
1.66-1.760.18411450.18563020X-RAY DIFFRACTION98.32
1.76-1.90.22541460.1893031X-RAY DIFFRACTION98.94
1.9-2.090.20451460.16913049X-RAY DIFFRACTION99.25
2.09-2.390.18171490.16463086X-RAY DIFFRACTION99.6
2.39-3.010.19721470.18253081X-RAY DIFFRACTION99.57
3.01-100.21741130.20342347X-RAY DIFFRACTION75.11
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)
16.27143636787-3.42593800798-1.64377703025.288791345661.179949634872.23565211895-0.0696863718829-0.117352371360.016915834076-0.03144176303970.1625030469990.2081105077890.005146709385880.0424260971574-0.07887356235270.0846807324516-0.019360769638-0.01687646577630.1131871145630.01267980248590.0813098590595.24661066626-4.016662281615.96911700626
21.488195338613.097201941422.258755490236.679470789944.624989837333.719902140330.00438835889857-0.1783967263430.08808114172350.310093255458-0.1558997163140.144726007577-0.0406214838021-0.2088553987440.1338616308820.157836077120.03877981876690.008724249044280.144067828797-0.01183658254650.14163642673810.03648226353.3734138685217.1750639655
33.318862044080.702836608005-1.493445655840.823174699009-0.08327019503185.56486735367-0.140439518338-0.0381351524073-0.015336240464-0.0335082746259-0.0422039501605-0.337361580708-0.1662026930150.1339455342030.1137090787810.174470346193-0.00274584165153-0.01886011236220.08808830903910.007398795327830.17573718143421.539726714412.875032747412.1090141698
42.482617662630.794339142999-0.03127541691765.092625130650.2277608253721.68947753006-0.119935047735-0.4207397875940.2077759912980.171167922403-0.08795710933910.327091035494-0.311062955568-0.2362812275240.2131180395310.1462791196460.0734133519637-0.006429323479920.227741709933-0.03246119503560.1685668432435.206764463512.381226799712.5680220867
51.10406671409-1.843277272160.09093033746239.227529242720.5713790250270.743120396129-0.01145245991940.0427772154209-0.00806429241445-0.0597614347320.0793596232065-0.1731176922880.02331001459690.0453042402832-0.06741056298120.099724921520.01420756437120.02012869025920.130347280723-0.01659346412330.095802379829517.1564607449-5.773465716547.88295632106
63.396761039611.982227872421.771160722566.623346789194.926790847723.70078778794-0.291823904598-0.6289261590130.279276424880.4197839186150.02815980318380.0579880087906-0.12603488771-0.2520798258650.2135136272670.266065653710.131934838786-0.06012055557880.268149761288-0.04242351294510.13607702980917.4854489447-8.8749050323317.2625156419
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 7 through 40 )BA7 - 401 - 34
22chain 'B' and (resid 41 through 69 )BA41 - 6935 - 63
33chain 'B' and (resid 70 through 101 )BA70 - 10164 - 95
44chain 'C' and (resid 7 through 29 )CB7 - 291 - 23
55chain 'C' and (resid 30 through 64 )CB30 - 6424 - 58
66chain 'C' and (resid 65 through 80 )CB65 - 8059 - 74

+
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