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- PDB-7da2: The crystal structure of the chicken FANCM-MHF complex -

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Basic information

Entry
Database: PDB / ID: 7da2
TitleThe crystal structure of the chicken FANCM-MHF complex
Components
  • Centromere protein S
  • Centromere protein X
  • Fanconi anemia group M protein
KeywordsDNA BINDING PROTEIN / Histone fold / DNA Binding / DNA / DNA repair / Fanconi Anemia / Nucleus / Hef ortholog
Function / homology
Function and homology information


PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / double-strand break repair via synthesis-dependent strand annealing / 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 ...PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / double-strand break repair via synthesis-dependent strand annealing / 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 / four-way junction helicase activity / nuclease activity / kinetochore assembly / 3'-5' DNA helicase activity / replication fork processing / interstrand cross-link repair / four-way junction DNA binding / kinetochore / RNA helicase activity / RNA helicase / protein heterodimerization activity / cell division / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / ERCC4 domain ...Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Fanconi anemia group M protein / Centromere protein S / Centromere protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsNishino, T. / Ito, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07279 Japan
Japan Society for the Promotion of Science (JSPS)20K06512 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
A: Centromere protein S
C: Centromere protein S
B: Centromere protein X
D: Centromere protein X
E: Fanconi anemia group M protein


Theoretical massNumber of molelcules
Total (without water)60,0795
Polymers60,0795
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21230 Å2
ΔGint-131 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.249, 78.469, 87.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Centromere protein S / CENP-S


Mass: 11875.330 Da / Num. of mol.: 2 / Mutation: A29C, A31C, A58C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPS, APITD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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) / Strain (production host): BL21(DE3) / References: UniProt: P0DJH7
#3: Protein Fanconi anemia group M protein / Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa ...Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa / FAAP250 / Protein Hef ortholog


Mass: 17604.803 Da / Num. of mol.: 1 / Mutation: A29C, A31C, A58C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FANCM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D5PRR9, RNA helicase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.03 Å3/Da / Density % sol: 39.55 %
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% PEG1000, 12.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→45.17 Å / Num. obs: 12641 / % possible obs: 99.32 % / Redundancy: 6 % / Biso Wilson estimate: 54.94 Å2 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.145 / Net I/σ(I): 32
Reflection shellResolution: 2.79→2.89 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 4.32 / Num. unique obs: 1232 / Rrim(I) all: 0.873

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Processing

Software
NameVersionClassification
HKL-20001.18.2_3874data processing
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b0b

3b0b


Resolution: 2.79→45.17 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2618 633 5.01 %
Rwork0.216 12008 -
obs0.2183 12641 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.05 Å2
Refinement stepCycle: LAST / Resolution: 2.79→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 0 47 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033868
X-RAY DIFFRACTIONf_angle_d0.52735201
X-RAY DIFFRACTIONf_chiral_restr0.0366585
X-RAY DIFFRACTIONf_plane_restr0.0061676
X-RAY DIFFRACTIONf_dihedral_angle_d22.9741483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-30.33051230.27332355X-RAY DIFFRACTION99.56
3-3.310.29351260.2532379X-RAY DIFFRACTION99.96
3.31-3.780.25791270.20962406X-RAY DIFFRACTION99.92
3.78-4.770.24421260.19092392X-RAY DIFFRACTION99.57
4.77-100.24891310.21162476X-RAY DIFFRACTION97.57
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)
17.392.9134.23322.55113.02547.43770.2597-0.4867-0.80650.15150.4268-0.0223-1.25-0.1357-0.74220.4222-0.04160.02980.32210.06630.41284.09556.77324.5466
21.35431.62591.19521.92240.93170.92130.57691.706-0.7281-0.24310.1313-0.1410.785-0.5502-0.3930.7412-0.1746-0.10450.96450.00870.8028-12.7681-33.67741.99
38.14511.4468-0.6595.0432-1.7391.92330.53-1.1182-1.08741.15190.04720.28070.0038-1.3878-0.33510.7287-0.0352-0.0130.68540.16320.446-9.273-22.466617.3153
40.8831-2.49291.74754.4513-3.83032.53090.7550.3056-0.44510.27720.46682.5910.1538-0.6864-0.54550.5344-0.03630.01490.79580.08271.0548-9.78273.2535.0611
53.9065-0.03320.32845.0871-1.75243.68330.2847-0.1989-0.05770.5663-0.41760.1729-0.0277-0.1275-0.12420.3899-0.1149-0.01170.53740.04170.29959.1508-0.97657.0237
64.25680.87-3.47624.9575-1.21252.7976-0.0851-0.57340.46351.0929-0.198-1.0462-1.21370.87930.2580.8182-0.09930.06340.5854-0.13290.720219.195821.0101-3.5585
79.4965-3.3631-2.90084.4597-0.57141.7253-1.24741.0505-0.8712-0.552-1.24950.4605-0.3585-2.2836-0.77020.31840.2949-0.06380.46250.05240.45715.932529.2651-2.5634
84.31350.18692.16291.96710.25064.5629-0.00810.0861-0.2122-0.1037-0.12120.26730.0105-0.2760.09640.2746-0.03660.03090.3945-0.01480.3496-5.9235-14.60121.5361
92.43541.52291.39919.79-0.45826.57820.09840.8969-0.253-0.2874-0.5965-1.7036-1.62071.17510.03760.4974-0.1063-0.05460.72950.10620.61572.5371-10.8047-13.5661
100.1305-0.84070.87125.0333-5.42695.88262.77671.8574-0.6666-1.7593-1.05780.51441.91230.9091-1.42010.94390.2286-0.23342.2079-0.66012.24318.2203-19.2144-12.6702
119.6561-0.2064-1.30615.65072.18184.81840.1088-0.21240.72690.29860.0543-0.1307-0.9879-0.0615-0.26740.52760.09850.01750.32150.03650.4059.644520.2236-4.1882
127.36476.07684.16298.80534.37134.5925-0.26650.777-0.3246-0.31780.9586-0.5828-0.10760.5772-0.40190.3968-0.00460.03430.47360.02440.24268.18996.5427-8.9854
135.91350.70440.6186.26962.57936.149-0.71550.41531.1155-0.3330.29650.98980.0155-0.58750.18870.3654-0.0876-0.07980.73310.13040.53-6.55075.0378-15.0905
144.9936-4.49981.97625.9388-5.58688.70920.75660.76680.1183-0.6984-0.7841-0.25160.5101-0.3691-0.12340.494-0.2309-0.0310.597-0.00140.4831-10.5041-19.8175-3.4914
157.7042.75941.6013.07653.47116.8681-0.95332.30411.80760.23360.84671.09690.2914-1.0263-0.23750.5559-0.1786-0.01330.87910.15620.6415-14.5697-12.3963-13.2432
165.92941.14272.48194.0028-0.57016.8201-0.02550.07420.00620.0325-0.35220.04080.49630.64630.04720.23590.02850.05340.414-0.00490.36646.5022-17.25465.1281
178.39170.3671-4.55113.5845-2.21734.0631-0.3874-0.48810.1580.14820.2813-0.17060.4381-0.66740.02220.2940.03170.06940.3554-0.02630.23666.6869-7.16857.1402
184.9555-5.3787-5.89115.46316.17676.94351.38041.67430.9506-0.8262-1.101-1.0988-0.8852-1.351-0.14280.4857-0.00390.12390.61870.24570.62258.487514.5324-17.3927
192.67290.5121-1.06198.62-0.59154.2092-0.31641.5392-0.7739-1.3897-0.8169-0.37450.2459-0.60040.02980.79590.06530.0171.04960.01070.4128.48153.7371-24.3354
204.82541.7841-2.3683.79321.75376.58050.6874-0.1570.18350.33760.42740.5553-0.7399-0.10230.31970.51050.15880.13030.49470.06760.45180.348915.04760.4903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 67 through 82 )D67 - 82
2X-RAY DIFFRACTION2chain 'E' and (resid 673 through 686 )E673 - 686
3X-RAY DIFFRACTION3chain 'E' and (resid 687 through 706 )E687 - 706
4X-RAY DIFFRACTION4chain 'E' and (resid 707 through 725 )E707 - 725
5X-RAY DIFFRACTION5chain 'E' and (resid 726 through 773 )E726 - 773
6X-RAY DIFFRACTION6chain 'E' and (resid 774 through 793 )E774 - 793
7X-RAY DIFFRACTION7chain 'E' and (resid 794 through 804 )E794 - 804
8X-RAY DIFFRACTION8chain 'A' and (resid 7 through 78 )A7 - 78
9X-RAY DIFFRACTION9chain 'A' and (resid 79 through 89 )A79 - 89
10X-RAY DIFFRACTION10chain 'A' and (resid 90 through 102 )A90 - 102
11X-RAY DIFFRACTION11chain 'C' and (resid 12 through 43 )C12 - 43
12X-RAY DIFFRACTION12chain 'C' and (resid 44 through 71 )C44 - 71
13X-RAY DIFFRACTION13chain 'C' and (resid 72 through 103 )C72 - 103
14X-RAY DIFFRACTION14chain 'B' and (resid 8 through 22 )B8 - 22
15X-RAY DIFFRACTION15chain 'B' and (resid 23 through 31 )B23 - 31
16X-RAY DIFFRACTION16chain 'B' and (resid 32 through 66 )B32 - 66
17X-RAY DIFFRACTION17chain 'B' and (resid 67 through 82 )B67 - 82
18X-RAY DIFFRACTION18chain 'D' and (resid 9 through 22 )D9 - 22
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 31 )D23 - 31
20X-RAY DIFFRACTION20chain 'D' and (resid 32 through 66 )D32 - 66

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