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- PDB-4day: Crystal structure of the RMI core complex with MM2 peptide from FANCM -

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Basic information

Entry
Database: PDB / ID: 4day
TitleCrystal structure of the RMI core complex with MM2 peptide from FANCM
Components
  • Fanconi anemia group M protein
  • RecQ-mediated genome instability protein 1
  • RecQ-mediated genome instability protein 2
Keywordsprotein binding/Hydrolase / OB fold / protein binding-Hydrolase complex
Function / homology
Function and homology information


regulation of sister chromatid segregation / double-strand break repair via synthesis-dependent strand annealing / RecQ family helicase-topoisomerase III complex / FANCM-MHF complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / Fanconi anaemia nuclear complex / maintenance of rDNA / resolution of meiotic recombination intermediates / nuclease activity ...regulation of sister chromatid segregation / double-strand break repair via synthesis-dependent strand annealing / RecQ family helicase-topoisomerase III complex / FANCM-MHF complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / Fanconi anaemia nuclear complex / maintenance of rDNA / resolution of meiotic recombination intermediates / nuclease activity / Impaired BRCA2 binding to PALB2 / positive regulation of protein monoubiquitination / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / 3'-5' DNA helicase activity / Impaired BRCA2 binding to RAD51 / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / response to glucose / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / four-way junction DNA binding / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PKR-mediated signaling / HDR through Homologous Recombination (HRR) / multicellular organism growth / glucose homeostasis / Processing of DNA double-strand break ends / four-way junction helicase activity / Regulation of TP53 Activity through Phosphorylation / DNA replication / RNA helicase activity / nuclear speck / nuclear body / RNA helicase / DNA repair / nucleotide binding / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / Helix Hairpins / Nucleic acid-binding proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helix non-globular / Special / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Fanconi anemia group M protein / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHoadley, K.A. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Defining the molecular interface that connects the Fanconi anemia protein FANCM to the Bloom syndrome dissolvasome.
Authors: Hoadley, K.A. / Xue, Y. / Ling, C. / Takata, M. / Wang, W. / Keck, J.L.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RecQ-mediated genome instability protein 1
B: RecQ-mediated genome instability protein 2
C: Fanconi anemia group M protein


Theoretical massNumber of molelcules
Total (without water)37,7693
Polymers37,7693
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-38 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.312, 96.440, 99.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein RecQ-mediated genome instability protein 1 / BLM-associated protein of 75 kDa / BLAP75 / FAAP75


Mass: 17401.254 Da / Num. of mol.: 1 / Fragment: C-terminal OB domain (residues 473-625)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI1, C9orf76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A7
#2: Protein RecQ-mediated genome instability protein 2 / hRMI2 / BLM-associated protein of 18 kDa / BLAP18


Mass: 16168.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI2, C16orf75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96E14
#3: Protein/peptide 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: 4199.458 Da / Num. of mol.: 1 / Fragment: MM2 peptide (residues 1218-1251)
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, RNA helicase

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 200 mM Na2SO4, 5% polyethylene glycol 3350, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 5728 / Num. obs: 5711 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.163 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.365.10.5872601.0291100
3.36-3.425.30.3822910.921199.7
3.42-3.485.20.382721.0671100
3.48-3.555.30.2782770.9651100
3.55-3.635.20.2652791.0471100
3.63-3.725.20.1862870.9571100
3.72-3.815.20.1732740.916199.6
3.81-3.915.10.1582881.0091100
3.91-4.035.20.1372921.0931100
4.03-4.165.20.1172871.182199.7
4.16-4.315.20.12681.3381100
4.31-4.485.10.0822871.4381100
4.48-4.6850.0792831.497199.6
4.68-4.935.20.0682941.4861100
4.93-5.245.10.0642801.2531100
5.24-5.6450.0652921.3121100
5.64-6.215.10.0522911.125199.7
6.21-7.150.0492931.1811100
7.1-8.944.90.0343001.24199.7
8.94-504.40.0263161.233196.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3mxn

3mxn


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.82 / WRfactor Rfree: 0.3042 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7471 / SU B: 75.396 / SU ML: 0.557 / SU R Cruickshank DPI: 0.4697 / SU Rfree: 0.6787 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.679 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3254 273 4.8 %RANDOM
Rwork0.2165 ---
all0.2552 5728 --
obs0.2217 5711 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.78 Å2 / Biso mean: 92.948 Å2 / Biso min: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å20 Å2
2---0.05 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 0 0 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222135
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9952885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0422485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2121515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211561
X-RAY DIFFRACTIONr_mcbond_it0.3751.51344
X-RAY DIFFRACTIONr_mcangle_it0.72922180
X-RAY DIFFRACTIONr_scbond_it0.9643791
X-RAY DIFFRACTIONr_scangle_it1.7484.5705
LS refinement shellResolution: 3.286→3.371 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 18 -
Rwork0.329 359 -
all-377 -
obs--97.16 %
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)
12.2813-0.89221.17333.2087-1.15254.8267-0.06310.241-0.33250.02730.02120.18270.2217-0.13360.04190.1566-0.01540.05430.0433-0.04450.068711.2933-6.81143.7276
25.8793-0.1754-1.21855.4824-1.78264.4032-0.0962-0.15630.39140.1208-0.01050.2627-0.2407-0.67750.10670.27770.1329-0.02010.1768-0.06810.06181.239910.66269.6541
39.9876-6.1070.398410.07340.46710.1701-0.218-0.6834-0.53220.7920.21110.52220.2195-0.21120.00690.80990.0802-0.02780.8229-0.02980.61227.0805-7.705220.0544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A482 - 625
2X-RAY DIFFRACTION2B13 - 147
3X-RAY DIFFRACTION3C1226 - 1237

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