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- PDB-7da1: Crystal structure of the chicken MHF complex -

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Basic information

Entry
Database: PDB / ID: 7da1
TitleCrystal 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 / 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 ...PKR-mediated signaling / 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: 2.01 Å
AuthorsIto, S. / Nishino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
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
A: Centromere protein S
D: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)42,4744
Polymers42,4744
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-91 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.432, 59.432, 220.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Centromere protein S / CENP-S


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


Mass: 9361.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPX, STRA13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DJH7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MOPS-HEPES pH 7.0, 0.1 M Carboxylic acids mix, 15% MPD, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→40.46 Å / Num. obs: 27614 / % possible obs: 99.85 % / Redundancy: 12.6 % / Biso Wilson estimate: 24.65 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 22.3
Reflection shellResolution: 2.01→2.082 Å / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3 / Num. unique obs: 2661 / Rpim(I) all: 0.217 / Rrim(I) all: 0.802

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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: 2.01→40.46 Å / SU ML: 0.1768 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 2000 7.24 %
Rwork0.1967 25614 -
obs0.1987 27614 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 171 2875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712730
X-RAY DIFFRACTIONf_angle_d0.90893663
X-RAY DIFFRACTIONf_chiral_restr0.0464430
X-RAY DIFFRACTIONf_plane_restr0.0048473
X-RAY DIFFRACTIONf_dihedral_angle_d4.6214374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.23541390.19781790X-RAY DIFFRACTION99.74
2.06-2.110.26731400.21431777X-RAY DIFFRACTION99.84
2.11-2.170.24871380.18891765X-RAY DIFFRACTION99.95
2.17-2.240.22621390.18471800X-RAY DIFFRACTION99.95
2.24-2.320.24171410.19841796X-RAY DIFFRACTION99.9
2.32-2.420.25521400.18681795X-RAY DIFFRACTION100
2.42-2.530.20111410.18841808X-RAY DIFFRACTION100
2.53-2.660.22281420.19111820X-RAY DIFFRACTION99.95
2.66-2.830.21571430.20131831X-RAY DIFFRACTION100
2.83-3.040.20911410.1921806X-RAY DIFFRACTION100
3.04-3.350.21481450.19671857X-RAY DIFFRACTION99.9
3.35-3.830.19881450.17881850X-RAY DIFFRACTION99.85
3.84-4.830.22531470.18811889X-RAY DIFFRACTION99.9
4.83-40.460.24261590.22932030X-RAY DIFFRACTION99.36
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)
11.796011001870.5064540287172.86936821553.17210064972-1.675112361097.41641390613-0.012273761312-0.200785959994-0.24315168062-0.0299962766034-0.00244499277481-0.2246433440510.188018516253-0.02595298925590.04957487036190.195389602325-0.003828187573080.06148474858080.1793980649680.03015468850810.165836133575-23.08395052364.38479825532.80904687306
27.444092361621.35857028167-2.523755555971.75720620456-1.320279077372.66481812224-0.410087193331-0.250110432466-1.089466054940.0177131424465-0.0487514738724-0.3296705714810.2018345374570.0734586201480.3812600581270.1501684123930.0304780732960.008644204174720.165161447840.002136040084720.160391203969-19.57151978454.18659610806-8.44828400088
35.060511318880.7770181362311.132863393763.09137233601-1.009350579913.23997230767-0.6061319567870.2180127981931.37714899919-0.002767104775630.3184578781330.61617599147-1.03669425691-0.4268010504290.06311924881040.2492959970720.102202606129-0.04233113741440.2896281528990.02607823399050.4545555569-15.345940092120.7504342171-13.9267403881
44.18650729212-3.39779630103-3.554786410694.614170643851.075251324665.57348886604-0.163589919161-1.050455000750.4523779181360.4245916075910.147275100635-0.19392657878-0.4433268738590.830587420067-0.0248361111010.208127061943-0.0562077327175-0.01955047389620.2575425130830.01024719524180.19644552636-13.53617528519.96161485734-0.122652290635
57.63537080870.282840756433-0.02758138395296.5171142384-0.2583443503763.48484922118-0.04057579323840.285086500853-0.484096064945-0.7883188636620.0989072275244-0.1303651416560.2231035612390.572071587818-0.05547818023050.164165330005-0.0191649840574-0.0007249922357450.2248043373670.004914296459850.204954194647-3.22596617719.21169909315-7.95592119829
69.259015968454.023238451661.807446604522.961954984740.8997259416921.099709767330.0893466347883-0.09416538801370.4665734391030.0782214039311-0.03030150505430.221662662908-0.0979402081153-0.1288123167060.01232439377880.1640564620040.01963114309180.03509465539670.1706298283760.0338290015680.155083205243-27.126586559611.0942208246-8.25939077634
76.23468308083-0.221709018401-4.395300032016.988395201742.853741908474.12776808968-0.0362144078443-0.490154047784-0.5505913357770.6400914606950.2629901660690.9835823893740.280241879671-0.8930553174970.3287906467960.216780049346-0.09052165527640.1031746406530.4425051138840.162278351820.484915043104-42.9247135388-1.61116042046-6.56826480966
87.43339629273-1.14052520532-0.2381537399532.812843604131.938318741156.78716674935-0.1612956323490.367798302941-0.449599209001-0.3696695280820.1619722172930.1268834126220.42781382474-0.05127950020520.1973778791640.1210693211770.0249220839640.007777508473040.1453632593250.01890241976870.147482783923-29.30291159141.22717845758-14.568263389
94.10344329967-0.222152186185-0.4247065844978.35945536755-2.21627969294.551087571120.0660777562831-0.05115276564550.15727042941-0.413069899673-0.23315654961-0.2829774883910.322194164877-0.1769944533840.1627384195970.111598628879-0.00524086358728-0.002859048251320.194531651307-0.05639639778720.111757221244-23.6763384506-0.392676417686-44.2585623834
103.576762262492.473526796432.340070259942.915682700041.60006327033.534803892180.14447384916-0.012191004699-0.3337271206880.0744016900504-0.0767647325198-0.3122158182440.2847304111370.2154184385130.01069626438290.1630466089840.02013386087740.03238785764050.2120136366370.03803426324670.191100910247-12.65438556245.81040848517-31.1203313522
113.514059661-1.47466744835-0.5872395813588.560295972993.237831357664.64769433485-0.006773916475890.437301121851-0.00719859438273-0.81102094396-0.0909338960694-0.441693090462-0.3923856681280.356585289020.1077867627910.194857022102-0.0238222839277-0.001576104184130.2844551055460.04108960615060.227675877793-14.19749762619.21810921129-42.4867003931
124.78577410489-1.027188316350.1444097174316.01086535136-0.2597780468073.202881556030.254124565604-0.2526712538590.1681320314780.152666355494-0.1772125816070.0837496926954-0.19105913559-0.208565380995-0.000601980916710.157121895079-0.008748231477330.01781278962390.2349899446930.03785866061880.150910082014-10.324992467719.1188384074-35.6413114249
138.0277343146.7298899913-1.28188009837.54059082683-0.3526961935223.63072886070.154737267222-0.573000280511-0.700158660760.29511162736-0.293739314958-0.604518447230.6185192299230.1483833289570.1690701509140.2536217929190.05452202348060.001967519654440.2144248253490.03863581767540.182698037052-17.455449522-4.23286958731-34.31176566
145.58677561542.82351029516-0.6930364330882.79823992304-1.879231152395.877603358790.0702848886724-0.182778129163-0.7567312227640.06975245451440.1565322380020.8507242361131.42067624246-0.968077366518-0.1415465087110.653069377188-0.3358070025480.08712172644960.683656592823-0.01996803140880.478975099311-34.4135748867-14.9603902265-35.7052436116
154.365909481280.9320789207851.439961751315.558221824881.468787313735.42111288305-0.23640037136-0.552542373024-0.1348896494010.2125693152940.07484444190360.05899618416540.202368345337-0.6100413434380.01436320618260.34509938641-0.03461600142320.07494280087090.338652625996-0.05462786073170.178277154704-27.2031614607-3.24582262893-27.585169208
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 8 through 35 )BA8 - 351 - 28
22chain 'B' and (resid 36 through 69 )BA36 - 6929 - 62
33chain 'B' and (resid 70 through 103 )BA70 - 10363 - 96
44chain 'C' and (resid 6 through 20 )CB6 - 201 - 15
55chain 'C' and (resid 21 through 29 )CB21 - 2916 - 24
66chain 'C' and (resid 30 through 57 )CB30 - 5725 - 52
77chain 'C' and (resid 58 through 64 )CB58 - 6453 - 59
88chain 'C' and (resid 65 through 80 )CB65 - 8060 - 75
99chain 'A' and (resid 9 through 40 )AC9 - 401 - 32
1010chain 'A' and (resid 41 through 100 )AC41 - 10033 - 92
1111chain 'D' and (resid 6 through 20 )DD6 - 201 - 15
1212chain 'D' and (resid 21 through 29 )DD21 - 2916 - 24
1313chain 'D' and (resid 30 through 57 )DD30 - 5725 - 52
1414chain 'D' and (resid 58 through 64 )DD58 - 6453 - 59
1515chain 'D' and (resid 65 through 80 )DD65 - 8060 - 75

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