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- PDB-6fc6: Bik1 CAP-Gly domain with ETF peptide from Bim1 -

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Basic information

Entry
Database: PDB / ID: 6fc6
TitleBik1 CAP-Gly domain with ETF peptide from Bim1
Components
  • Nuclear fusion protein BIK1
  • Protein BIM1
KeywordsCELL CYCLE / +TIP / Bik1 / CAP-Gly / Bim1 / ETF / yeast
Function / homology
Function and homology information


mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / protein localization to microtubule plus-end / mitotic spindle elongation / cell tip / nuclear migration along microtubule / microtubule plus-end / negative regulation of microtubule depolymerization ...mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / protein localization to microtubule plus-end / mitotic spindle elongation / cell tip / nuclear migration along microtubule / microtubule plus-end / negative regulation of microtubule depolymerization / microtubule plus-end binding / mating projection tip / mitotic sister chromatid cohesion / spindle pole body / negative regulation of microtubule polymerization / microtubule associated complex / microtubule depolymerization / establishment of mitotic spindle orientation / spindle assembly / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule organization / cytoplasmic microtubule / positive regulation of microtubule polymerization / spindle midzone / kinetochore / microtubule organizing center / spindle microtubule / spindle / spindle pole / cell cortex / microtubule binding / cell division / nucleus / cytoplasm
Similarity search - Function
EB1-C terminal (EB1-C) domain profile. / CAP-Gly domain signature. / EB1, C-terminal domain superfamily / Microtubule-associated protein RP/EB / EB1, C-terminal / EB1-like C-terminal motif / CAP_GLY / CAP-Gly domain profile. / CAP-Gly domain / CAP Gly-rich domain superfamily ...EB1-C terminal (EB1-C) domain profile. / CAP-Gly domain signature. / EB1, C-terminal domain superfamily / Microtubule-associated protein RP/EB / EB1, C-terminal / EB1-like C-terminal motif / CAP_GLY / CAP-Gly domain profile. / CAP-Gly domain / CAP Gly-rich domain superfamily / CAP Gly-rich domain / Calponin homology (CH) domain profile. / Calponin homology domain / CH domain superfamily
Similarity search - Domain/homology
Nuclear fusion protein BIK1 / Protein BIM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, A. / Stangier, M.M. / Steinmetz, M.O.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
SystemsX.chRTD-TubeX Switzerland
Marie CurieCOFUND fellowship Switzerland
CitationJournal: Structure / Year: 2018
Title: Structure-Function Relationship of the Bik1-Bim1 Complex.
Authors: Stangier, M.M. / Kumar, A. / Chen, X. / Farcas, A.M. / Barral, Y. / Steinmetz, M.O.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear fusion protein BIK1
B: Protein BIM1


Theoretical massNumber of molelcules
Total (without water)12,6522
Polymers12,6522
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-1 kcal/mol
Surface area4920 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)53.566, 53.566, 62.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nuclear fusion protein BIK1 /


Mass: 11357.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BIK1, YCL029C, YCL29C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P11709
#2: Protein/peptide Protein BIM1


Mass: 1294.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40013
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4 / Details: 0.1 M sodium cacodylate, 1.0 M sodium citrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40.55 Å / Num. obs: 8808 / % possible obs: 100 % / Redundancy: 25.3 % / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.87 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bik1 CAP-Gly domain (PDB ID: 6FC5)
Resolution: 1.8→40.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.768 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 881 10 %RANDOM
Rwork0.185 ---
obs0.1894 7926 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 33.25 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.8→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 0 55 716
Biso mean---42.63 -
Num. residues----86
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02673
X-RAY DIFFRACTIONr_bond_other_d0.0020.02657
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.979902
X-RAY DIFFRACTIONr_angle_other_deg1.04531508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.868584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.86924.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60415118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.383153
X-RAY DIFFRACTIONr_chiral_restr0.1140.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 65 -
Rwork0.37 580 -
all-645 -
obs--99.69 %

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