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- PDB-1ukv: Structure of RabGDP-dissociation inhibitor in complex with prenyl... -

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Basic information

Entry
Database: PDB / ID: 1ukv
TitleStructure of RabGDP-dissociation inhibitor in complex with prenylated YPT1 GTPase
Components
  • GTP-binding protein YPT1
  • Secretory pathway GDP dissociation inhibitor
KeywordsPROTEIN TRANSPORT / GTPase / Hydrolase / GDP dissociation inhibitor / vesicular transport
Function / homology
Function and homology information


pre-mRNA catabolic process / Rab GDP-dissociation inhibitor activity / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport ...pre-mRNA catabolic process / Rab GDP-dissociation inhibitor activity / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle budding / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / phagophore assembly site membrane / Golgi stack / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endocytic recycling / phagophore assembly site / reticulophagy / SNARE complex assembly / small GTPase-mediated signal transduction / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / SNARE binding / macroautophagy / intracellular protein transport / protein transport / cytoplasmic vesicle / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / mitochondrion / cytosol / cytoplasm
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 Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / FAD/NAD(P)-binding domain ...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 Rab1 family 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 / Rab subfamily of small GTPases / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GERAN-8-YL GERAN / GTP-binding protein YPT1 / Rab GDP-dissociation inhibitor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRak, A. / Pylypenko, O. / Durek, T. / Watzke, A. / Kushnir, S. / Brunsveld, L. / Waldmann, H. / Goody, R.S. / Alexandrov, K.
CitationJournal: Science / Year: 2003
Title: Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase
Authors: Rak, A. / Pylypenko, O. / Durek, T. / Watzke, A. / Kushnir, S. / Brunsveld, L. / Waldmann, H. / Goody, R.S. / Alexandrov, K.
History
DepositionSep 1, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
G: Secretory pathway GDP dissociation inhibitor
Y: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4495
Polymers74,7072
Non-polymers7423
Water16,430912
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-25 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.503, 119.577, 60.723
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules GY

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


Mass: 51466.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19tev / 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 YPT1 / YPT1 GTPase


Mass: 23240.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PTWIN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01123

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Non-polymers , 4 types, 915 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 912 / 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: 2.01 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8000, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 106322 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.072 / Net I/σ(I): 11.65
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.59 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 18312 / Rsym value: 0.405 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1590335.92 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5317 5 %RANDOM
Rwork0.192 ---
obs0.192 106322 98.3 %-
all-106322 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5513 Å2 / ksol: 0.315519 e/Å3
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5165 0 49 912 6126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.632
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 866 5 %
Rwork0.26 16452 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP_CGE_PEG.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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