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- PDB-3cph: Crystal structure of Sec4 in complex with Rab-GDI -

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Basic information

Entry
Database: PDB / ID: 3cph
TitleCrystal structure of Sec4 in complex with Rab-GDI
Components
  • Rab GDP-dissociation inhibitor
  • Ras-related protein SEC4
KeywordsPROTEIN TRANSPORT / Rab GTPase / prenylation / vesicular transport / Cytoplasm / Cytoplasmic vesicle / Exocytosis / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Palmitate / Phosphoprotein / GTPase activation
Function / homology
Function and homology information


Rab GDP-dissociation inhibitor activity / membrane addition at site of cytokinesis / ascospore-type prospore assembly / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / cellular bud neck / Golgi to plasma membrane transport / mating projection tip ...Rab GDP-dissociation inhibitor activity / membrane addition at site of cytokinesis / ascospore-type prospore assembly / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / cellular bud neck / Golgi to plasma membrane transport / mating projection tip / small GTPase-mediated signal transduction / transport vesicle membrane / exocytosis / transport vesicle / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / autophagy / protein transport / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / : / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / : / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / 3-Layer(bba) Sandwich / Rab subfamily of small GTPases / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein SEC4 / Rab GDP-dissociation inhibitor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKravchenko, S. / Ignatev, A. / Goody, R.S. / Rak, A. / Pylypenko, O.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
Authors: Ignatev, A. / Kravchenko, S. / Rak, A. / Goody, R.S. / Pylypenko, O.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
G: Rab GDP-dissociation inhibitor
A: Ras-related protein SEC4
H: Rab GDP-dissociation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3365
Polymers125,8693
Non-polymers4682
Water1,56787
1
G: Rab GDP-dissociation inhibitor
A: Ras-related protein SEC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0654
Polymers74,5982
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-25.3 kcal/mol
Surface area27800 Å2
MethodPISA
2
H: Rab GDP-dissociation inhibitor


Theoretical massNumber of molelcules
Total (without water)51,2711
Polymers51,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.900, 131.900, 217.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Rab GDP-dissociation inhibitor / Rab GDI / Secretory pathway GDP dissociation inhibitor / yeast Rab-GDI


Mass: 51271.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39958
#2: Protein Ras-related protein SEC4 / Suppressor of RHO3 protein 6 / small GTPase Sec4


Mass: 23326.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07560
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.34 Å3/Da / Density % sol: 71.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG MME 2000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9816 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9816 Å / Relative weight: 1
ReflectionResolution: 2.9→19.9 Å / Num. all: 49236 / Num. obs: 48896 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.95 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ukv, chain G

1ukv


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.504 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26763 2437 5 %RANDOM
Rwork0.21773 ---
all0.2202 46245 --
obs0.2202 46245 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8373 0 29 87 8489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228582
X-RAY DIFFRACTIONr_bond_other_d0.0010.025879
X-RAY DIFFRACTIONr_angle_refined_deg1.121.97511604
X-RAY DIFFRACTIONr_angle_other_deg0.824314400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87951049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02924.674383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.469151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2841537
X-RAY DIFFRACTIONr_chiral_restr0.0610.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021689
X-RAY DIFFRACTIONr_nbd_refined0.1990.21713
X-RAY DIFFRACTIONr_nbd_other0.1790.25762
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24115
X-RAY DIFFRACTIONr_nbtor_other0.0820.24496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1390.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.23
X-RAY DIFFRACTIONr_mcbond_it0.6161.56794
X-RAY DIFFRACTIONr_mcbond_other0.051.52132
X-RAY DIFFRACTIONr_mcangle_it0.67528473
X-RAY DIFFRACTIONr_scbond_it0.71434003
X-RAY DIFFRACTIONr_scangle_it1.1354.53131
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 181 -
Rwork0.333 3291 -
obs--99.71 %

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