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- PDB-4bxo: Architecture and DNA recognition elements of the Fanconi anemia F... -

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Basic information

Entry
Database: PDB / ID: 4bxo
TitleArchitecture and DNA recognition elements of the Fanconi anemia FANCM- FAAP24 complex
Components
  • 5'-D(*GP*AP*TP*GP*AP*TP*GP*CP*TP*GP*CP)-3'
  • 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*AP*TP*CP)-3'
  • FANCONI ANEMIA GROUP M PROTEIN
  • FANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA BINDING / PSEUDO-NUCLEASE
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / four-way junction helicase activity / resolution of meiotic recombination intermediates / nuclease activity / 3'-5' DNA helicase activity / positive regulation of protein monoubiquitination / replication fork processing / interstrand cross-link repair ...double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / four-way junction helicase activity / resolution of meiotic recombination intermediates / nuclease activity / 3'-5' DNA helicase activity / positive regulation of protein monoubiquitination / 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
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 / SAD / Resolution: 2.15 Å
AuthorsCoulthard, R. / Deans, A. / Swuec, P. / Bowles, M. / Purkiss, A. / Costa, A. / West, S. / McDonald, N.
CitationJournal: Structure / Year: 2013
Title: Architecture and DNA Recognition Elements of the Fanconi Anemia Fancm-Faap24 Complex.
Authors: Coulthard, R. / Deans, A.J. / Swuec, P. / Bowles, M. / Costa, A. / West, S.C. / Mcdonald, N.Q.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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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-ASSOCIATED PROTEIN OF 24 KDA
H: 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*AP*TP*CP)-3'
I: 5'-D(*GP*AP*TP*GP*AP*TP*GP*CP*TP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6908
Polymers59,5294
Non-polymers1604
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-91.2 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.100, 125.100, 74.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein FANCONI ANEMIA GROUP M PROTEIN / PROTEIN FACM / ATP-DEPENDENT RNA HELICASE FANCM / FANCONI ANE MIA-ASSOCIATED POLYPEPTIDE OF 250 KDA ...PROTEIN FACM / ATP-DEPENDENT RNA HELICASE FANCM / FANCONI ANE MIA-ASSOCIATED POLYPEPTIDE OF 250 KDA / FAAP250 / PROTEIN HEF ORTHOL OG / FANCM


Mass: 28771.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): FB810 / References: UniProt: Q8IYD8, RNA helicase
#2: Protein FANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDA / FAAP24


Mass: 24050.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): FB810 / References: UniProt: Q9BTP7

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DNA chain , 2 types, 2 molecules HI

#3: DNA chain 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*AP*TP*CP)-3'


Mass: 3413.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*GP*AP*TP*GP*AP*TP*GP*CP*TP*GP*CP)-3'


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 104 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGSGS FROM VECTOR AT N-TERMINUS GSH FROM VECTOR AT N-TERMINUS SYNTHETIC DNA CONSTRUCT

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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: 3.26 Å3/Da / Density % sol: 62.3 % / Description: NATIVE DATA
Crystal growpH: 8
Details: 18%W/V PEG 3350, 0.2M CALCIUM ACETATE, 0.01M BARIUM CHLORIDE., pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 2006 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30.34 Å / Num. obs: 32846 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
BNPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→25.43 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.54 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUAL U VALUES ONLY. CHAIN A RESIDUES 1799-1817, 1963-1968, 2036-2048 HAVE NO VISIBLE ELECTRON DENSITY CHAIN B RESIDUES 1-11, 147-153 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUAL U VALUES ONLY. CHAIN A RESIDUES 1799-1817, 1963-1968, 2036-2048 HAVE NO VISIBLE ELECTRON DENSITY CHAIN B RESIDUES 1-11, 147-153 HAVE NO VISIBLE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25523 1645 5.1 %RANDOM
Rwork0.2036 ---
obs0.20615 30696 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→25.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 445 4 100 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9832.1284984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30525.276127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6441512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212501
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7121.51982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11123209
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.72331631
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3234.51774
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 130 -
Rwork0.209 2183 -
obs--100 %
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)
14.1926-2.15940.7682.26960.30222.9198-0.0731-0.10890.22250.02710.0462-0.0325-0.2133-0.02470.02690.09910.0207-0.0240.0083-0.01830.062644.045104.74768.663
21.732-0.3401-0.79124.96262.01485.1085-0.0118-0.0465-0.19830.27280.0511-0.00090.3424-0.0357-0.03930.13160.05120.00360.1101-0.01660.101331.988112.52289.732
34.7947-0.09951.49792.7044-0.17351.66480.0587-0.2321-0.14190.168-0.0441-0.23360.10660.1648-0.01460.02680.0104-0.00360.06010.00660.063661.54588.11569.059
43.6561-1.2474-0.17814.92160.91293.9947-0.0014-0.10840.06480.0353-0.01160.0129-0.0383-0.19340.0130.07450.0336-0.00620.0715-0.03570.022326.583126.57993.43
53.3869-0.2859-0.8635.8598-0.448811.92510.15050.9980.7441-0.80870.081-0.5136-0.70710.1722-0.23150.44890.0652-0.00390.48680.0280.38226.933139.81979.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1818 - 1962
2X-RAY DIFFRACTION2A1969 - 2035
3X-RAY DIFFRACTION3B12 - 146
4X-RAY DIFFRACTION4B154 - 214
5X-RAY DIFFRACTION5H1 - 11
6X-RAY DIFFRACTION5I1 - 11

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