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- PDB-2bcg: Structure of doubly prenylated Ypt1:GDI complex -

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Basic information

Entry
Database: PDB / ID: 2bcg
TitleStructure of doubly prenylated Ypt1:GDI complex
Components
  • GTP-binding protein YPT1
  • Secretory pathway GDP dissociation inhibitor
KeywordsPROTEIN TRANSPORT / RabGTPase / geranylgeranylation / 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-coated vesicle budding / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / phagophore assembly site membrane / Golgi stack / cis-Golgi network / endocytic recycling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / reticulophagy / SNARE complex assembly / small GTPase-mediated signal transduction / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / SNARE binding / macroautophagy / intracellular protein transport / protein transport / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / 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: 1.48 Å
AuthorsPylypenko, O. / Rak, A. / Alexandrov, K.
CitationJournal: Embo J. / Year: 2006
Title: Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling
Authors: Pylypenko, O. / Rak, A. / Durek, T. / Kushnir, S. / Dursina, B.E. / Thomae, N.H. / Constantinescu, A.T. / Brunsveld, L. / Watzke, A. / Waldmann, H. / Goody, R.S. / Alexandrov, K.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.5Aug 23, 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: Secretory pathway GDP dissociation inhibitor
Y: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8917
Polymers74,7532
Non-polymers1,1395
Water16,628923
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.660, 120.230, 60.550
Angle α, β, γ (deg.)90.00, 90.67, 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


Mass: 51466.430 Da / Num. of mol.: 1 / Fragment: RabGDI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GDI1 / 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 YPT1 / Protein YP2


Mass: 23286.318 Da / Num. of mol.: 1 / Fragment: YPT1 / Mutation: G204C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPT1 / Plasmid: pTWIN-1 / 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 , 5 types, 928 molecules

#3: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H34
#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 / 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 14% PEG MME 2000, 100 mM Tris-Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.48→19.92 Å / Num. all: 113100 / Num. obs: 109178 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24 Å2 / Rsym value: 0.076 / Net I/σ(I): 11.32
Reflection shellResolution: 1.48→1.49 Å / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ukv

1ukv


Resolution: 1.48→19.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.609 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.071 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19283 5459 5 %RANDOM
Rwork0.16336 ---
all0.16486 109178 --
obs0.16486 103719 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.48→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 77 923 6268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225448
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9837360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.765634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49524.845258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.621151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6651527
X-RAY DIFFRACTIONr_chiral_restr0.0960.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024012
X-RAY DIFFRACTIONr_nbd_refined0.2060.22645
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2759
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.244
X-RAY DIFFRACTIONr_mcbond_it1.3451.53297
X-RAY DIFFRACTIONr_mcangle_it225249
X-RAY DIFFRACTIONr_scbond_it2.91932454
X-RAY DIFFRACTIONr_scangle_it3.6964.52111
X-RAY DIFFRACTIONr_rigid_bond_restr2.13735751
X-RAY DIFFRACTIONr_sphericity_free5.6363924
X-RAY DIFFRACTIONr_sphericity_bonded3.80435345
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 316
Rwork0.198 6020

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