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- PDB-4m6w: Crystal structure of the C-terminal segment of FANCM in complex w... -

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Basic information

Entry
Database: PDB / ID: 4m6w
TitleCrystal structure of the C-terminal segment of FANCM in complex with FAAP24
Components
  • Fanconi anemia group M protein
  • Fanconi anemia-associated protein of 24 kDa
KeywordsDNA BINDING PROTEIN / FANCM / FAAP24 / XPF/Mus81 / Fanconi anemia / DNA repair
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 / four-way junction helicase activity / nuclease activity / positive regulation of protein monoubiquitination / 3'-5' DNA helicase activity / replication fork processing / interstrand cross-link repair ...double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / four-way junction helicase activity / 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 / 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, DEAH-box helicase domain / : / FANCM pseudonuclease domain / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM to MHF binding domain / Rossmann fold - #10130 / ERCC4 domain ...Fanconi anemia-associated protein of 24kDa / Fanconi anemia core complex-associated protein 24, pseudonuclease domain / FANCM, DEAH-box helicase domain / : / FANCM pseudonuclease domain / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM to MHF binding domain / Rossmann fold - #10130 / 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 / DEAD/DEAH box helicase domain / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fanconi anemia group M protein / Fanconi anemia core complex-associated protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsYang, H. / Zhang, T. / Tong, L. / Ding, J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair.
Authors: Yang, H. / Zhang, T. / Tao, Y. / Wang, F. / Tong, L. / Ding, J.
History
DepositionAug 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi anemia group M protein
B: Fanconi anemia-associated protein of 24 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8185
Polymers48,5302
Non-polymers2883
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-68 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.174, 98.111, 140.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 25132.857 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1813-2031
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8IYD8, RNA helicase
#2: Protein Fanconi anemia-associated protein of 24 kDa


Mass: 23397.285 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAAP24, C19orf40 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9BTP7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.0M (NH4)2SO4, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796, 0.9795, 0.9792, 0.9568
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97951
30.97921
40.95681
ReflectionResolution: 2.9→50 Å / Num. obs: 12155 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.8 / Num. unique all: 12155 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.492 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.299 598 4.9 %RANDOM
Rwork0.2544 ---
obs0.2567 11554 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.7 Å2 / Biso mean: 69.7247 Å2 / Biso min: 34.52 Å2
Baniso -1Baniso -2Baniso -3
1-5.53 Å20 Å20 Å2
2---2 Å2-0 Å2
3----3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 15 8 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193113
X-RAY DIFFRACTIONr_bond_other_d0.0020.023089
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.9744200
X-RAY DIFFRACTIONr_angle_other_deg0.83737092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1635383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95924.818137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.07515587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4781518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 39 -
Rwork0.332 821 -
all-860 -
obs--95.34 %

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