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- PDB-9hjo: FANCM-FAAP24-dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 9hjo
TitleFANCM-FAAP24-dsDNA complex
Components
  • (DNA (25-MER)) x 2
  • (Fanconi anemia ...) x 2
KeywordsDNA BINDING PROTEIN / Fanconia Anemia / DNA Interstrand Crosslink repair / Nucleic acid binding / Helix-hairpin-Helix
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 / intracellular membrane-bounded organelle / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Fanconi anemia-associated protein of 24kDa / Fanconi anemia core complex-associated protein 24, pseudonuclease domain / FANCM pseudonuclease domain / 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 ...Fanconi anemia-associated protein of 24kDa / Fanconi anemia core complex-associated protein 24, pseudonuclease domain / FANCM pseudonuclease domain / 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 / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / 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 / Fanconi anemia core complex-associated protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsCoulthard-Graf, R.J. / Briggs, D.C. / McDonald, N.Q. / Deans, A.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1181110 Australia
The Francis Crick InstituteCC2068 United Kingdom
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
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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
B: Fanconi anemia core complex-associated protein 24
C: Fanconi anemia group M protein
D: Fanconi anemia core complex-associated protein 24
F: DNA (25-MER)
G: DNA (25-MER)
H: DNA (25-MER)
I: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,56912
Polymers132,4728
Non-polymers974
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, On gel Filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-131 kcal/mol
Surface area44410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.008, 69.975, 86.76
Angle α, β, γ (deg.)91.629, 89.929, 115.952
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D
53F
63H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRASPASPAA1818 - 20384 - 224
211THRTHRASPASPCC1818 - 20384 - 224
322PROPROPROPROBB15 - 21415 - 214
422PROPROPROPRODD15 - 21415 - 214
533DADADCDCFE9 - 199 - 19
633DADADCDCHG9 - 199 - 19

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Fanconi anemia ... , 2 types, 4 molecules ACBD

#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: 26989.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Certain Cys residues have been modified by 2'mercaptoethanol adducts
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Production host: Escherichia coli (E. coli) / Strain (production host): FB810 / References: UniProt: Q8IYD8, RNA helicase
#2: Protein Fanconi anemia core complex-associated protein 24 / Fanconi anemia-associated protein of 24 kDa


Mass: 23924.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAAP24, C19orf40 / Production host: Escherichia coli (E. coli) / Strain (production host): FB810 / References: UniProt: Q9BTP7

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DNA chain , 2 types, 4 molecules FHGI

#3: DNA chain DNA (25-MER)


Mass: 7600.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (25-MER)


Mass: 7720.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 118 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350 0.1M di-ammonium monohydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryocooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.4→86.72 Å / Num. obs: 48487 / % possible obs: 96.2 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rpim(I) all: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1780 / CC1/2: 0.344 / Rpim(I) all: 0.928 / % possible all: 70.19

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→86.718 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.179 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / ESU R: 0.352 / ESU R Free: 0.261
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1979 4.084 %Random
Rwork0.2145 46479 --
all0.217 ---
obs-48458 96.147 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.968 Å2-1.416 Å2-0.144 Å2
2---2.152 Å2-0.639 Å2
3---3.634 Å2
Refinement stepCycle: LAST / Resolution: 2.401→86.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 859 4 114 7392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127513
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166951
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.82210309
X-RAY DIFFRACTIONr_angle_other_deg0.6511.73816027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.77542
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.574535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.529101237
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.92210295
X-RAY DIFFRACTIONr_chiral_restr0.0780.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028091
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021628
X-RAY DIFFRACTIONr_nbd_refined0.1850.21378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1440.26395
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23441
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.24145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2199
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.211
X-RAY DIFFRACTIONr_nbd_other0.0920.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.29
X-RAY DIFFRACTIONr_mcbond_it3.3453.7853236
X-RAY DIFFRACTIONr_mcbond_other3.3453.7853236
X-RAY DIFFRACTIONr_mcangle_it5.356.7964031
X-RAY DIFFRACTIONr_mcangle_other5.356.7964032
X-RAY DIFFRACTIONr_scbond_it5.0685.6654277
X-RAY DIFFRACTIONr_scbond_other5.0675.6664278
X-RAY DIFFRACTIONr_scangle_it7.81110.3586271
X-RAY DIFFRACTIONr_scangle_other7.81110.3596272
X-RAY DIFFRACTIONr_lrange_it9.82952.1598302
X-RAY DIFFRACTIONr_lrange_other9.82951.6978290
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.056570
X-RAY DIFFRACTIONr_ncsr_local_group_20.080.055798
X-RAY DIFFRACTIONr_ncsr_local_group_30.1280.05887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.090910.05009
12CX-RAY DIFFRACTIONLocal ncs0.090910.05009
23BX-RAY DIFFRACTIONLocal ncs0.080430.05009
24DX-RAY DIFFRACTIONLocal ncs0.080430.05009
35FX-RAY DIFFRACTIONLocal ncs0.127620.05011
36HX-RAY DIFFRACTIONLocal ncs0.127620.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.401-2.4630.431080.38326230.38537400.8770.8973.02140.375
2.463-2.530.4071500.36932530.37136230.8790.90393.92770.354
2.53-2.6040.3591610.32532580.32735070.9060.9397.49070.302
2.604-2.6840.3991400.30232590.30634810.910.94597.64440.273
2.684-2.7720.278960.25331690.25433260.9530.9698.1660.22
2.772-2.8690.3231110.2630080.26231810.9370.95998.05090.221
2.869-2.9770.2651280.24529360.24631240.9560.96498.07940.206
2.977-3.0980.2671170.2327840.23129550.9540.96898.17260.196
3.098-3.2360.2891060.23227690.23529270.9430.9798.22340.206
3.236-3.3940.2381360.22125160.22126930.9680.97598.47750.199
3.394-3.5770.2291090.19424590.19526060.9780.98398.54180.178
3.577-3.7930.243710.18423640.18624660.9730.98298.74290.167
3.793-4.0550.272970.17422030.17823350.9580.98198.50110.153
4.055-4.3790.216930.16820330.1721510.9690.98398.83780.151
4.379-4.7960.228760.16418600.16619570.9650.98498.92690.148
4.796-5.360.239980.18116900.18518100.9720.98498.78450.162
5.36-6.1850.253770.19714800.215770.9770.9898.73180.179
6.185-7.5650.335360.22212830.22513330.9270.97298.94970.201
7.565-10.6580.209500.1669740.16810270.9760.98499.70790.178
10.658-86.7180.29190.285580.2815810.9420.94699.31150.295
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)
11.5730.9961.73213.071.39543.098-0.227-0.09340.01310.13320.1017-0.1121-0.17410.06140.12530.0660.036-0.00990.0643-0.02310.04960.8935-44.918441.1293
21.84090.46621.75381.46841.41565.5898-0.0784-0.4189-0.10550.45150.0785-0.0190.1355-0.1774-0.00020.23190.06340.03070.1365-0.01470.1501-0.5308-48.675353.7146
31.7482-1.0025-1.69593.12791.45393.0473-0.21060.0864-0.0149-0.14010.1394-0.10710.2190.0340.07110.10530.0005-0.03410.0372-0.03140.06310.7948-15.737727.6399
41.9912-0.3979-1.64851.52991.33395.248-0.09520.46320.0536-0.45810.069-0.0332-0.1597-0.160.02620.2299-0.0567-0.09160.1332-0.01020.1532-0.5626-12.010715.0986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp1818 - 2038
2X-RAY DIFFRACTION2ALLBp15 - 214
3X-RAY DIFFRACTION3ALLCp1818 - 2038
4X-RAY DIFFRACTION4ALLDp15 - 214

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