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- PDB-2g77: Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase... -

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Basic information

Entry
Database: PDB / ID: 2g77
TitleCrystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3
Components
  • GTPase-activating protein GYP1
  • Ras-related protein Rab-33B
KeywordsHYDROLASE ACTIVATOR/PROTEIN TRANSPORT / Protein transport / Gyp1 TBC domain / Rab33 / vesicular trafficking / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / regulation of Golgi organization / Intra-Golgi traffic / Rab protein signal transduction / protein localization to Golgi apparatus / intra-Golgi vesicle-mediated transport / Golgi stack ...negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / regulation of Golgi organization / Intra-Golgi traffic / Rab protein signal transduction / protein localization to Golgi apparatus / intra-Golgi vesicle-mediated transport / Golgi stack / skeletal system morphogenesis / activation of GTPase activity / autophagosome assembly / GTPase activator activity / presynapse / vesicle-mediated transport / intracellular protein transport / Golgi lumen / protein transport / endosome / GTPase activity / Golgi membrane / GTP binding / Golgi apparatus / mitochondrion
Similarity search - Function
Rab33A/B / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / TBC/rab GAP domain profile. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / small GTPase Rab1 family profile. / Cyclin A; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases ...Rab33A/B / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / TBC/rab GAP domain profile. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / small GTPase Rab1 family profile. / Cyclin A; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-33B / ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / GTPase-activating protein GYP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å
AuthorsPan, X. / Eathiraj, S. / Munson, M. / Lambright, D.G.
CitationJournal: Nature / Year: 2006
Title: TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism.
Authors: Pan, X. / Eathiraj, S. / Munson, M. / Lambright, D.G.
History
DepositionFeb 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
A: GTPase-activating protein GYP1
B: Ras-related protein Rab-33B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2595
Polymers70,7082
Non-polymers5513
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-21 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)72.200, 94.526, 102.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is same as protein complex in the asymmetric unit

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GTPase-activating protein GYP1 / GAP for YPT1


Mass: 48158.516 Da / Num. of mol.: 1 / Fragment: Gyp1 TBC domain / Mutation: E405K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: GYP1 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL Codon Plus / References: UniProt: Q08484
#2: Protein Ras-related protein Rab-33B


Mass: 22549.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab33b / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL Codon Plus / References: UniProt: O35963

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Non-polymers , 4 types, 419 molecules

#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 / 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
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: 10~15% polyethylene glycol 6000, 100 mM Sodium Acetate, 10% Glycerol, 20 mM NaF, 2mM AlCl3, 50 mM HEPES, pH7.0, EVAPORATION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.979026
SYNCHROTRONNSLS X29A20.9793, 0.9790, 0.9670
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 9, 2005
ADSC QUANTUM 3152CCDFeb 9, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790261
20.97931
30.9791
40.9671
ReflectionResolution: 2.26→50 Å / Num. all: 62674 / Num. obs: 33046 / % possible obs: 99 % / Observed criterion σ(F): 37.6 / Observed criterion σ(I): 1017 / Redundancy: 5 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.065 / Net I/σ(I): 9.9
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.93 / Num. unique all: 6309 / Rsym value: 0.354 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.26→8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.205 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24357 1634 5.1 %RANDOM
Rwork0.20524 ---
all0.207 ---
obs0.20726 30553 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.538 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20 Å2
2--4.63 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.26→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 33 416 4590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9425805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7135501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86924215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16615738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3931528
X-RAY DIFFRACTIONr_chiral_restr0.0690.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023241
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.22166
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22938
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5191.52626
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91224107
X-RAY DIFFRACTIONr_scbond_it0.81731935
X-RAY DIFFRACTIONr_scangle_it1.324.51696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.262→2.316 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 112 -
Rwork0.238 2072 -
obs--97.46 %

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