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- PDB-2doq: crystal structure of Sfi1p/Cdc31p complex -

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Basic information

Entry
Database: PDB / ID: 2doq
Titlecrystal structure of Sfi1p/Cdc31p complex
Components
  • Cell division control protein 31
  • SFI1p
KeywordsCELL CYCLE / Sfi1p / centrin / cdc31p / spindle pole body / centrosome
Function / homology
Function and homology information


half bridge of spindle pole body / spindle pole body duplication / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / spindle assembly / mRNA export from nucleus / spindle pole / G2/M transition of mitotic cell cycle / nuclear envelope ...half bridge of spindle pole body / spindle pole body duplication / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / spindle assembly / mRNA export from nucleus / spindle pole / G2/M transition of mitotic cell cycle / nuclear envelope / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cell division / calcium ion binding / positive regulation of transcription by RNA polymerase II / identical protein binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1000 / Sfi1 spindle body / Spindle body associated protein, C-terminal domain / Sfi1 spindle body protein / Spindle body associated protein C-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1000 / Sfi1 spindle body / Spindle body associated protein, C-terminal domain / Sfi1 spindle body protein / Spindle body associated protein C-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division control protein 31 / Protein SFI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsLi, S. / Sandercock, A.M. / Conduit, P.T. / Robinson, C.V. / Williams, R.L. / Kilmartin, J.V.
CitationJournal: J.Cell Biol. / Year: 2006
Title: Structural role of Sfi1p-centrin filaments in budding yeast spindle pole body duplication.
Authors: Li, S. / Sandercock, A.M. / Conduit, P. / Robinson, C.V. / Williams, R.L. / Kilmartin, J.V.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 31
B: Cell division control protein 31
C: Cell division control protein 31
D: SFI1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84411
Polymers68,5644
Non-polymers2817
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-153 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.283, 92.961, 189.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cell division control protein 31 / Nucleoporin CDC31 / Nuclear pore protein CDC31


Mass: 19055.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC31 / Plasmid: pGEX6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P06704
#2: Protein SFI1p


Mass: 11397.563 Da / Num. of mol.: 1 / Fragment: Residues: 218 - 306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SFI1 / Plasmid: pGEX6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q12369
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 56.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 9% iso-propanol, 0.1M MES pH=6.2, 0.2M Ca(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794, 0.9393
DetectorType: ADSC / Detector: CCD / Date: Nov 21, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.93931
ReflectionResolution: 3.25→94.49 Å / Num. obs: 12505 / % possible obs: 99.7 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 3.8
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.013 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→94.49 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 48.46 / SU ML: 0.449 / Cross valid method: THROUGHOUT / σ(F): 1.1 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29899 785 5 %RANDOM
Rwork0.25857 ---
obs0.26057 14942 99.49 %-
all-14942 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å20 Å2
2--0.62 Å20 Å2
3----3.75 Å2
Refinement stepCycle: LAST / Resolution: 3→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 7 4 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224287
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.975743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56925.341249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.35415832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8251526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023263
X-RAY DIFFRACTIONr_nbd_refined0.2510.22256
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2176
X-RAY DIFFRACTIONr_metal_ion_refined0.20.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.26
X-RAY DIFFRACTIONr_mcbond_it0.6261.52574
X-RAY DIFFRACTIONr_mcangle_it0.83624030
X-RAY DIFFRACTIONr_scbond_it1.2931881
X-RAY DIFFRACTIONr_scangle_it1.8714.51713
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 65 -
Rwork0.353 1061 -
obs--98.51 %

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