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- PDB-4drb: The crystal structure of FANCM bound MHF complex -

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Basic information

Entry
Database: PDB / ID: 4drb
TitleThe crystal structure of FANCM bound MHF complex
Components
  • Centromere protein S
  • Centromere protein X
  • Fanconi anemia group M protein
KeywordsDNA BINDING PROTEIN/PROTEIN BINDING / DNA repair / DNA binding complex / Histone fold / DNA damage repair / DNA binding / DNA BINDING-PROTEIN BINDING complex / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / nuclease activity / kinetochore assembly / inner kinetochore / positive regulation of protein monoubiquitination / 3'-5' DNA helicase activity / replication fork processing ...double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / nuclease activity / kinetochore assembly / inner kinetochore / positive regulation of protein monoubiquitination / 3'-5' DNA helicase activity / replication fork processing / interstrand cross-link repair / four-way junction DNA binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / positive regulation of protein ubiquitination / chromosome segregation / Fanconi Anemia Pathway / RHO GTPases Activate Formins / PKR-mediated signaling / Separation of Sister Chromatids / four-way junction helicase activity / RNA helicase activity / RNA helicase / protein heterodimerization activity / cell division / DNA repair / DNA damage response / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / Centromere protein X / CENP-S/Mhf1 ...Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / 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 / Histone, subunit A / Histone, subunit A / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein X / Fanconi anemia group M protein / Centromere protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.634 Å
AuthorsTao, Y. / Niu, L. / Teng, M.
CitationJournal: Nat Commun / Year: 2012
Title: The structure of the FANCM-MHF complex reveals physical features for functional assembly
Authors: Tao, Y. / Jin, C. / Li, X. / Qi, S. / Chu, L. / Niu, L. / Yao, X. / Teng, M.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centromere protein S
B: Centromere protein S
C: Fanconi anemia group M protein
D: Centromere protein S
E: Centromere protein S
F: Fanconi anemia group M protein
G: Centromere protein S
H: Centromere protein S
I: Fanconi anemia group M protein
J: Centromere protein X
K: Centromere protein X
L: Centromere protein X
M: Centromere protein X
N: Centromere protein X
O: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)192,58215
Polymers192,58215
Non-polymers00
Water2,162120
1
A: Centromere protein S
B: Centromere protein S
C: Fanconi anemia group M protein
J: Centromere protein X
K: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)64,1945
Polymers64,1945
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18710 Å2
ΔGint-158 kcal/mol
Surface area19510 Å2
MethodPISA
2
D: Centromere protein S
E: Centromere protein S
F: Fanconi anemia group M protein
L: Centromere protein X
M: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)64,1945
Polymers64,1945
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17680 Å2
ΔGint-162 kcal/mol
Surface area18240 Å2
MethodPISA
3
G: Centromere protein S
H: Centromere protein S
I: Fanconi anemia group M protein
N: Centromere protein X
O: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)64,1945
Polymers64,1945
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18300 Å2
ΔGint-155 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.317, 70.025, 115.751
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Centromere protein S / CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold ...CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold protein 1 / Fanconi anemia-associated polypeptide of 16 kDa


Mass: 14325.699 Da / Num. of mol.: 6 / Fragment: C-terminus deleted, UNP residues 1-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APITD1, CENPS, FAAP16, MHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N2Z9
#2: 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: 16845.693 Da / Num. of mol.: 3 / Fragment: MHF binding domain, UNP residues 661-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYD8
#3: Protein
Centromere protein X / CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa ...CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa / Retinoic acid-inducible gene D9 protein homolog / Stimulated by retinoic acid gene 13 protein homolog


Mass: 9348.481 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STRA13, CENPX, FAAP10, MHF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MT69
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 0.2 M (NH4)2SO4, 25% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.634→50 Å / Num. obs: 52925 / % possible obs: 100 % / Biso Wilson estimate: 40.36 Å2
Reflection shellResolution: 2.634→2.73 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.62 / Num. unique all: 5221 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.634→49.67 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8165 / SU ML: 0.35 / σ(F): 0 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 2559 5.07 %
Rwork0.2205 --
obs0.2223 50516 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.932 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 102.71 Å2 / Biso mean: 44.9905 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1--7.8686 Å20 Å21.3622 Å2
2--5.7781 Å2-0 Å2
3---2.0905 Å2
Refinement stepCycle: LAST / Resolution: 2.634→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10363 0 0 120 10483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210543
X-RAY DIFFRACTIONf_angle_d0.53914268
X-RAY DIFFRACTIONf_dihedral_angle_d17.9643714
X-RAY DIFFRACTIONf_chiral_restr0.0391681
X-RAY DIFFRACTIONf_plane_restr0.0021841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6344-2.72860.33122380.2791425486
2.7286-2.83780.35372380.2725449690
2.8378-2.96690.30062270.2661458992
2.9669-3.12330.30452790.2553471294
3.1233-3.3190.30172540.2422482196
3.319-3.57520.24422690.2226489298
3.5752-3.93480.23052660.197495199
3.9348-4.50390.20292540.1795502299
4.5039-5.67310.22052480.191506699
5.6731-49.6790.23632860.2102515499

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