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- PDB-3viq: Crystal structure of Swi5-Sfr1 complex from fission yeast -

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Basic information

Entry
Database: PDB / ID: 3viq
TitleCrystal structure of Swi5-Sfr1 complex from fission yeast
Components
  • Mating-type switching protein swi5
  • Swi5-dependent recombination DNA repair protein 1
KeywordsRECOMBINATION ACTIVATOR
Function / homology
Function and homology information


negative regulation of DNA recombinase disassembly / meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / regulation of reciprocal meiotic recombination / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly ...negative regulation of DNA recombinase disassembly / meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / regulation of reciprocal meiotic recombination / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly / double-strand break repair involved in meiotic recombination / DNA strand invasion / mitotic intra-S DNA damage checkpoint signaling / ATPase activator activity / positive regulation of DNA binding / chromosome segregation / double-strand break repair via homologous recombination / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / identical protein binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #1020 / SFR1/Mei5 family / Double-strand recombination repair protein / DNA repair protein, Swi5 / Swi5 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
NITRATE ION / Swi5-dependent recombination DNA repair protein 1 / Mating-type switching protein swi5
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKuwabara, N. / Murayama, Y. / Hashimoto, H. / Kokabu, Y. / Ikeguchi, M. / Sato, M. / Mayanagi, K. / Tsutsui, Y. / Iwasaki, H. / Shimizu, T.
CitationJournal: Structure / Year: 2012
Title: Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex
Authors: Kuwabara, N. / Murayama, Y. / Hashimoto, H. / Kokabu, Y. / Ikeguchi, M. / Sato, M. / Mayanagi, K. / Tsutsui, Y. / Iwasaki, H. / Shimizu, T.
History
DepositionOct 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 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: Swi5-dependent recombination DNA repair protein 1
B: Mating-type switching protein swi5
C: Swi5-dependent recombination DNA repair protein 1
D: Mating-type switching protein swi5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,60913
Polymers47,8064
Non-polymers8039
Water2,954164
1
A: Swi5-dependent recombination DNA repair protein 1
B: Mating-type switching protein swi5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1495
Polymers23,9032
Non-polymers2463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-44 kcal/mol
Surface area14130 Å2
MethodPISA
2
C: Swi5-dependent recombination DNA repair protein 1
D: Mating-type switching protein swi5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4608
Polymers23,9032
Non-polymers5576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-53 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.159, 128.682, 59.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Swi5-dependent recombination DNA repair protein 1 / DNA repair protein dds20 / Meiotically up-regulated gene 13 protein


Mass: 14139.093 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h- / Gene: sfr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USV1
#2: Protein Mating-type switching protein swi5 / DNA repair protein swi5


Mass: 9764.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h- / Gene: swi5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUB7

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Non-polymers , 4 types, 173 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEGMME2000, 0.2M sodium acetate, 0.2M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33408 / Num. obs: 33341 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0113refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.446 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 1752 5 %RANDOM
Rwork0.23044 ---
all0.23224 33671 --
obs0.23224 33341 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--1.54 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 51 164 3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223300
X-RAY DIFFRACTIONr_bond_other_d0.0010.022344
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9664411
X-RAY DIFFRACTIONr_angle_other_deg0.87435717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78825.085177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27315665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8721527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 116 -
Rwork0.28 2129 -
obs--93.74 %
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)
10.35090.1623-0.27680.1424-0.27520.73470.1107-0.12720.11450.0745-0.04560.0118-0.1869-0.1608-0.06510.3583-0.00390.00070.277-0.01410.33121.6019-16.2112-14.414
20.29120.06660.43370.23540.45673.73230.0682-0.0999-0.0491-0.0355-0.0557-0.03260.0783-0.2779-0.01250.0426-0.0353-0.00920.091-0.00020.038913.6309-31.8268-17.5643
31.1494-0.5260.27370.4911-0.25511.31420.1876-0.1887-0.382-0.1928-0.05810.2930.3538-0.2798-0.12950.3548-0.1353-0.07080.28190.08320.403624.976216.1382-4.7414
42.374-1.3133-2.82791.25791.51955.47960.0218-0.1738-0.07840.08950.00920.16270.1426-0.1185-0.0310.044-0.0612-0.00920.16080.05920.174517.920930.7793-3.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A178 - 299
2X-RAY DIFFRACTION2B1 - 85
3X-RAY DIFFRACTION3C184 - 299
4X-RAY DIFFRACTION4D13 - 85

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