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- PDB-7da0: High-resolution crystal structure of the chicken MHF complex -

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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


Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex ...Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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