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- PDB-2gv5: crystal structure of Sfi1p/Cdc31p complex -

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Basic information

Entry
Database: PDB / ID: 2gv5
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
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 - #1760 / EF-hand / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif ...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 - #1760 / EF-hand / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / 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 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 31
B: Cell division control protein 31
C: Sfi1p
D: Cell division control protein 31
E: Cell division control protein 31
F: Sfi1p


Theoretical massNumber of molelcules
Total (without water)94,0806
Polymers94,0806
Non-polymers00
Water95553
1
A: Cell division control protein 31
B: Cell division control protein 31
C: Sfi1p


Theoretical massNumber of molelcules
Total (without water)47,0403
Polymers47,0403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-46 kcal/mol
Surface area21350 Å2
MethodPISA
2
D: Cell division control protein 31
E: Cell division control protein 31
F: Sfi1p


Theoretical massNumber of molelcules
Total (without water)47,0403
Polymers47,0403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-46 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.775, 104.735, 184.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA15 - 16115 - 161
21SERSERDD15 - 16115 - 161
12SERSERBB15 - 16115 - 161
22SERSEREE15 - 16115 - 161
13LYSGLUCC643 - 7106 - 73
23LYSGLUFF643 - 7106 - 73

NCS ensembles :
ID
1
2
3

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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.: 4
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: 8929.131 Da / Num. of mol.: 2 / Fragment: Residues: 643-710
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9797, 0.9799, 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
30.91841
ReflectionResolution: 3→92.45 Å / Num. all: 34711 / Num. obs: 34711 / % possible obs: 99.9 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1.5 / Redundancy: 7.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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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→92.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 33.389 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.3 / ESU R: 0.566 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29654 1827 5 %RANDOM
Rwork0.25307 ---
obs0.25522 34711 99.98 %-
all-34711 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.434 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--2.64 Å20 Å2
3----6.06 Å2
Refinement stepCycle: LAST / Resolution: 3→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 0 53 6175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226214
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.988320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5915732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2725.35357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.569151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5321540
X-RAY DIFFRACTIONr_chiral_restr0.0760.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024712
X-RAY DIFFRACTIONr_nbd_refined0.2020.22917
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.25
X-RAY DIFFRACTIONr_mcbond_it0.4781.53752
X-RAY DIFFRACTIONr_mcangle_it0.6625868
X-RAY DIFFRACTIONr_scbond_it1.15132703
X-RAY DIFFRACTIONr_scangle_it1.6574.52452
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1211tight positional0.020.05
2B1211tight positional0.020.05
3C594tight positional0.020.05
1A1211tight thermal0.030.5
2B1211tight thermal0.030.5
3C594tight thermal0.030.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 126 -
Rwork0.404 2533 -
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)
14.43462.873-0.12152.22591.79439.62630.21780.0381-0.43110.0251-0.413-0.15570.74620.33350.1952-0.3020.1493-0.0018-0.20260.0383-0.275829.50737.698161.018
26.3417-1.26190.03539.67310.39716.4638-0.05770.61630.1256-0.04120.1715-0.1929-0.04840.3499-0.1137-0.4387-0.0639-0.0121-0.07370.0933-0.50910.31851.546137.561
33.77312.0857-1.0665.35-0.87710.7359-0.0176-0.1572-0.7546-0.3045-0.20870.0131.84130.11110.22630.11060.00850.03540.06560.06-0.172314.64342.867111.114
45.06930.38360.021110.9443-4.622510.9908-0.256-0.0026-0.010.396-0.0398-0.6939-1.03511.08130.2959-0.2074-0.1199-0.06480.06120.0217-0.425321.79966.4893.151
53.0598-2.131613.03292.4868-8.745955.6229-0.27660.16330.31080.22340.1171-0.0713-0.66040.35580.1595-0.49640.0218-0.0144-0.1287-0.0007-0.470319.67752.509147.586
62.83640.6287-8.6290.9229-6.178751.0996-0.03540.46-0.0676-0.2589-0.35010.14050.57450.78830.3855-0.15380.0547-0.01780.18190.1192-0.426323.71456.96496.957
74.9961-2.0845-0.82771.8973-1.89959.94830.212-0.1268-0.5420.1377-0.43530.0941.0716-0.33790.2233-0.2084-0.18180.0426-0.172-0.0597-0.2465-29.50637.79455.035
85.90230.8810.43810.462-1.74676.2402-0.1884-0.53210.06240.10870.21350.29480.146-0.1495-0.0252-0.45160.04190.0202-0.1063-0.0981-0.4976-10.251.56378.509
93.1804-1.3746-0.86335.14791.379613.4178-0.10150.2346-0.69670.3193-0.1122-0.12962.4301-0.0560.21370.09860.04090.0479-0.0685-0.009-0.1516-14.49242.826104.94
105.5489-0.44191.92729.56271.958712.1198-0.1701-0.34190.08070.1581-0.03230.4759-0.4585-0.66620.2023-0.50270.1069-0.0185-0.2070.0119-0.3499-21.46766.468122.875
113.12731.983912.19881.47528.90853.8955-0.1753-0.01350.1704-0.2406-0.03170.1654-1.0077-0.32760.2071-0.42120.0098-0.0262-0.1427-0.0132-0.4444-19.65452.61768.525
124.4893-1.332-12.48512.18738.350271.8256-0.0991-0.4083-0.0790.5078-0.3684-0.241.1075-0.45490.4675-0.3428-0.10390.0036-0.168-0.021-0.3526-23.55957.077119.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 9315 - 93
2X-RAY DIFFRACTION2AA94 - 16194 - 161
3X-RAY DIFFRACTION3BB15 - 9315 - 93
4X-RAY DIFFRACTION4BB94 - 16194 - 161
5X-RAY DIFFRACTION5CC643 - 6726 - 35
6X-RAY DIFFRACTION6CC675 - 71038 - 73
7X-RAY DIFFRACTION7DD15 - 9315 - 93
8X-RAY DIFFRACTION8DD94 - 16194 - 161
9X-RAY DIFFRACTION9EE15 - 9315 - 93
10X-RAY DIFFRACTION10EE94 - 16194 - 161
11X-RAY DIFFRACTION11FF643 - 6726 - 35
12X-RAY DIFFRACTION12FF675 - 71038 - 73

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