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- PDB-3cpj: Crystal structure of Ypt31 in complex with yeast Rab-GDI -

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Basic information

Entry
Database: PDB / ID: 3cpj
TitleCrystal structure of Ypt31 in complex with yeast Rab-GDI
Components
  • GTP-binding protein YPT31/YPT8
  • Rab GDP-dissociation inhibitor
KeywordsPROTEIN TRANSPORT / Rab GTPase / prenylation / vesicular transport / Acetylation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Cytoplasm / GTPase activation / Phosphoprotein
Function / homology
Function and homology information


Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network ...Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network / recycling endosome / autophagy / protein transport / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / mitochondrion / 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 / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...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 / 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 / GTP-binding protein YPT31/YPT8 / Rab GDP-dissociation inhibitor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Rab GDP-dissociation inhibitor
B: GTP-binding protein YPT31/YPT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3186
Polymers75,7792
Non-polymers5384
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-52.1 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.940, 61.430, 92.750
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules GB

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


Mass: 51271.230 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: P39958
#2: Protein GTP-binding protein YPT31/YPT8 / Rab GTPase YPT31


Mass: 24508.014 Da / Num. of mol.: 1 / Mutation: D58E
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: P38555

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Non-polymers , 4 types, 456 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.931 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.35→19.79 Å / Num. all: 30772 / Num. obs: 30683 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.35→2.4 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ukv, chain G

1ukv


Resolution: 2.35→19.79 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.523 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25523 1512 5 %RANDOM
Rwork0.19875 ---
all0.20156 28714 --
obs0.20156 28714 100 %-
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: 42.168 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 31 452 5232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224875
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9736594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73924.398216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04115850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9341523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023625
X-RAY DIFFRACTIONr_nbd_refined0.190.22231
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2420
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_mcbond_it0.4721.53075
X-RAY DIFFRACTIONr_mcangle_it0.83224807
X-RAY DIFFRACTIONr_scbond_it1.07932065
X-RAY DIFFRACTIONr_scangle_it1.7914.51787
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 109 -
Rwork0.231 2072 -
obs--100 %

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