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- PDB-9el5: FANCM translocase domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 9el5
TitleFANCM translocase domain bound to DNA
Components
  • DNA (37-MER)
  • Fanconi anemia group M protein
KeywordsNUCLEAR PROTEIN / Translocase / DNA-damage repair / ATPase / DNA-binding
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 / positive regulation of protein monoubiquitination / 3'-5' DNA helicase activity / replication fork processing / interstrand cross-link repair / four-way junction DNA binding ...double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / nuclease activity / positive regulation of protein monoubiquitination / 3'-5' DNA helicase activity / replication fork processing / interstrand cross-link repair / four-way junction DNA binding / Fanconi Anemia Pathway / PKR-mediated signaling / four-way junction helicase activity / RNA helicase activity / RNA helicase / chromatin binding / chromatin / ATP hydrolysis activity / nucleoplasm / ATP binding / 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 / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like ...Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / 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 / 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
DNA / DNA (> 10) / Fanconi anemia group M protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBythell-Douglas, R. / Murphy, V. / Deans, A.J. / Abbouche, L. / Wolf, J. / Rigoreau, L. / Chapman, K.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1181110 Australia
CitationJournal: Embo J. / Year: 2025
Title: Structural basis of Fanconi anemia pathway activation by FANCM.
Authors: Bythell-Douglas, R. / van Twest, S. / Abbouche, L. / Dunn, E. / Coulthard, R.J. / Briggs, D.C. / Murphy, V. / Zhang, X. / Tan, W. / Henrikus, S.S. / Qian, D. / Wu, Y. / Wolf, J. / Rigoreau, ...Authors: Bythell-Douglas, R. / van Twest, S. / Abbouche, L. / Dunn, E. / Coulthard, R.J. / Briggs, D.C. / Murphy, V. / Zhang, X. / Tan, W. / Henrikus, S.S. / Qian, D. / Wu, Y. / Wolf, J. / Rigoreau, L. / Shakeel, S. / Chapman, K.L. / McDonald, N.Q. / Deans, A.J.
History
DepositionDec 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fanconi anemia group M protein
P: DNA (37-MER)


Theoretical massNumber of molelcules
Total (without water)78,5492
Polymers78,5492
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-35 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.940, 89.840, 93.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: 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: 65232.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IYD8, RNA helicase
#2: DNA chain DNA (37-MER)


Mass: 13316.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 32.5% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.2→61.24 Å / Num. obs: 35277 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.023 / Rrim(I) all: 0.086 / Χ2: 1 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.236 / Num. measured all: 41340 / Num. unique obs: 2994 / CC1/2: 0.844 / Rpim(I) all: 0.344 / Rrim(I) all: 1.283 / Χ2: 0.96 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→61.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.527 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26697 1708 4.8 %RANDOM
Rwork0.21999 ---
obs0.22224 33512 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.153 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å2-0 Å2
2--3.04 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: 1 / Resolution: 2.2→61.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 761 0 80 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154714
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.667293
X-RAY DIFFRACTIONr_angle_other_deg1.0741.57410868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.81521.411241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6321536
X-RAY DIFFRACTIONr_chiral_restr0.0850.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021199
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4815.4822169
X-RAY DIFFRACTIONr_mcbond_other2.4785.4812168
X-RAY DIFFRACTIONr_mcangle_it3.9798.22713
X-RAY DIFFRACTIONr_mcangle_other3.9798.2022714
X-RAY DIFFRACTIONr_scbond_it2.836.383116
X-RAY DIFFRACTIONr_scbond_other2.836.383116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5629.4864581
X-RAY DIFFRACTIONr_long_range_B_refined7.09965.6626117
X-RAY DIFFRACTIONr_long_range_B_other7.165.6616112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 103 -
Rwork0.295 2448 -
obs--100 %

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