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- PDB-3s4w: Structure of the FANCI-FANCD2 complex -

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Basic information

Entry
Database: PDB / ID: 3s4w
TitleStructure of the FANCI-FANCD2 complex
Components
  • Fanconi anemia group D2 protein homolog
  • Fanconi anemia group I protein homolog
KeywordsDNA BINDING PROTEIN / dna repair
Function / homology
Function and homology information


Fanconi Anemia Pathway / regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / regulation of DNA-binding transcription factor activity / DNA repair complex ...Fanconi Anemia Pathway / regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / regulation of DNA-binding transcription factor activity / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / positive regulation of protein ubiquitination / response to gamma radiation / cellular response to oxidative stress / regulation of inflammatory response / nuclear body / DNA repair / DNA damage response / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 ...Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease
Similarity search - Domain/homology
Fanconi anemia group D2 protein homolog / Fanconi anemia group I protein homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.408 Å
AuthorsPavletich, N.P.
CitationJournal: Science / Year: 2011
Title: Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway.
Authors: Joo, W. / Xu, G. / Persky, N.S. / Smogorzewska, A. / Rudge, D.G. / Buzovetsky, O. / Elledge, S.J. / Pavletich, N.P.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 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: Fanconi anemia group I protein homolog
B: Fanconi anemia group D2 protein homolog


Theoretical massNumber of molelcules
Total (without water)297,2482
Polymers297,2482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-11 kcal/mol
Surface area107970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.800, 110.400, 350.500
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 I protein homolog / Protein FACI


Mass: 147120.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fanci / References: UniProt: Q8K368
#2: Protein Fanconi anemia group D2 protein homolog / Protein FACD2


Mass: 150127.234 Da / Num. of mol.: 1 / Fragment: unp residues 33-1415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fancd2 / References: UniProt: Q80V62

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM Hepes-Na, 40 mM potassium citrate, 10 mM DTT, 7 to 8 % (w/v) PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 45162 / Num. obs: 42995 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.9
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.8 / % possible all: 74

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3S51

3s51


Resolution: 3.408→19.858 Å / SU ML: 0.83 / σ(F): 0 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 1637 4.03 %
Rwork0.2396 --
obs0.241 40654 89.97 %
all-42995 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.21 Å2 / ksol: 0.275 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.1916 Å20 Å20 Å2
2--11.4363 Å20 Å2
3---6.7554 Å2
Refinement stepCycle: LAST / Resolution: 3.408→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18671 0 0 0 18671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418991
X-RAY DIFFRACTIONf_angle_d0.88125659
X-RAY DIFFRACTIONf_dihedral_angle_d16.677068
X-RAY DIFFRACTIONf_chiral_restr0.0653046
X-RAY DIFFRACTIONf_plane_restr0.0033217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4085-3.50820.401760.39632092X-RAY DIFFRACTION58
3.5082-3.62080.3811160.3382536X-RAY DIFFRACTION72
3.6208-3.74940.36051320.31022908X-RAY DIFFRACTION82
3.7494-3.89840.30141450.2823145X-RAY DIFFRACTION89
3.8984-4.07440.31271210.26333344X-RAY DIFFRACTION92
4.0744-4.28720.26731380.24053419X-RAY DIFFRACTION96
4.2872-4.55280.24021260.21593489X-RAY DIFFRACTION97
4.5528-4.89940.25731580.21323532X-RAY DIFFRACTION98
4.8994-5.38350.2911390.23963549X-RAY DIFFRACTION98
5.3835-6.14230.31351490.28943590X-RAY DIFFRACTION98
6.1423-7.66390.26721690.26743649X-RAY DIFFRACTION99
7.6639-19.85860.21381680.16993764X-RAY DIFFRACTION99
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)
12.3596-1.43620.87941.92860.22332.14220.37890.3779-0.3783-0.5862-0.26250.84010.5393-0.5732-0.00041.4738-0.2199-0.57991.29010.10231.1541-28.483335.5789.36
23.50572.22521.13362.8681-0.60732.3947-0.21680.1609-0.1551-0.27550.52810.50210.31810.1540.00481.02880.0528-0.19070.67490.02610.4087-2.778331.896735.7035
33.70241.32061.01282.299-0.3472.3879-0.0394-0.0005-0.176-0.3123-0.1621-0.14210.05260.11470.0010.706-0.0176-0.13470.50060.1080.419111.593736.436448.5922
41.09460.5730.58060.35230.19050.5491-0.03750.4534-0.4662-0.34890.212-0.00530.3112-0.5474-00.8389-0.2023-0.06190.90360.21930.608235.643551.532651.2479
53.40380.4608-0.39523.5677-2.87195.34680.00370.26140.2137-0.479-0.0196-0.35420.48920.1921-0.01090.3884-0.01670.00690.14410.02580.515750.708449.672164.9391
62.36131.1936-0.01873.6453-0.81463.4653-0.0802-0.34860.00880.47020.0891-0.0157-0.2821-0.35870.00470.3614-0.0853-0.03540.2441-0.0160.365544.517842.502887.5199
76.66931.51790.81371.63180.47140.59190.1878-0.3035-0.4482-0.0607-0.10380.13280.10810.05030.0120.37780.0239-0.04320.14080.09710.512713.375417.00876.1844
83.47791.7331-0.79941.3361-0.2940.2097-0.06410.20660.0441-0.2442-0.34920.4738-0.2289-0.191-0.03240.69550.1323-0.15320.7262-0.17941.2465-28.462914.104872.0244
96.182-1.35371.86111.8113-0.16392.207-0.1850.10210.6194-0.22990.1186-0.2738-0.1734-0.06240.00020.7721-0.04790.1140.67270.14840.763654.307967.303551.6432
103.3220.84452.22171.33290.31262.3018-0.03240.181-0.10780.05540.280.0227-0.03610.43050.05550.42530.1944-0.33990.66340.23150.14441.245461.334829.5725
110.8277-0.40370.59571.19960.38431.3270.56740.5897-0.5592-0.5608-0.04810.11330.73610.51160.04650.88710.0919-0.28550.88080.13970.4331-22.499160.85423.3679
120.66260.21891.17992.98360.20582.11920.010.4540.38570.13580.07740.2932-0.1798-0.3664-0.01380.6141-0.0147-0.13681.1880.5550.7429-38.44878.38484.9898
131.1934-1.3220.63192.49331.02253.1798-0.41550.12140.24240.3987-0.0739-0.399-0.0128-0.1005-0.13420.50830.0569-0.20450.88740.46980.6303-30.156883.174714.9608
142.22011.67520.55462.26880.13092.6108-0.37080.22160.39660.02650.0876-0.2021-0.09470.5183-0.01190.6297-0.0867-0.3550.83010.34230.7475-13.913290.166320.5834
151.5397-0.51931.63872.49120.72742.4501-0.5841-0.21550.92030.40680.1159-0.3225-0.66190.0595-0.00361.0652-0.1127-0.52470.6910.09271.1453-11.0897100.877137.769
160.2762-0.48980.31691.61550.83022.942-0.1372-0.5856-0.5440.27130.0961-0.469-0.0323-0.04070.00011.3526-0.1409-0.29411.0995-0.08731.3911-4.66794.9866.6158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:225)
2X-RAY DIFFRACTION2chain 'A' and (resseq 226:319)
3X-RAY DIFFRACTION3chain 'A' and (resseq 320:469)
4X-RAY DIFFRACTION4chain 'A' and (resseq 470:544)
5X-RAY DIFFRACTION5chain 'A' and (resseq 545:696)
6X-RAY DIFFRACTION6chain 'A' and (resseq 697:817)
7X-RAY DIFFRACTION7chain 'A' and (resseq 818:1186)
8X-RAY DIFFRACTION8chain 'A' and (resseq 1187:1300)
9X-RAY DIFFRACTION9chain 'B' and (resseq 43:337)
10X-RAY DIFFRACTION10chain 'B' and (resseq 338:565)
11X-RAY DIFFRACTION11chain 'B' and (resseq 566:662)
12X-RAY DIFFRACTION12chain 'B' and (resseq 663:797)
13X-RAY DIFFRACTION13chain 'B' and (resseq 798:959)
14X-RAY DIFFRACTION14chain 'B' and (resseq 960:1090)
15X-RAY DIFFRACTION15chain 'B' and (resseq 1091:1228)
16X-RAY DIFFRACTION16chain 'B' and (resseq 1229:1391)

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