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- PDB-3rwo: Crystal structure of YPT32 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 3rwo
TitleCrystal structure of YPT32 in complex with GDP
ComponentsGTP-binding protein YPT32/YPT11
KeywordsPROTEIN TRANSPORT / GTPASES / PROTEIN-GDP COMPLEX / EXOCYTOSIS / GOLGI APPARATUS / GTP-BINDING / LIPOPROTEIN / MEMBRANE / NUCLEOTIDE-BINDING / PRENYLATION / TRANSPORT / Ypt32 / Rab GTPase / GDP / vesicle trafficking / Myo2p / effectors
Function / homology
Function and homology information


Anchoring of the basal body to the plasma membrane / RAB geranylgeranylation / early endosome to Golgi transport / cellular bud neck / exocytosis / vesicle-mediated transport / recycling endosome / autophagy / protein transport / mitochondrial outer membrane ...Anchoring of the basal body to the plasma membrane / RAB geranylgeranylation / early endosome to Golgi transport / cellular bud neck / exocytosis / vesicle-mediated transport / recycling endosome / autophagy / protein transport / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein YPT32/YPT11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSultana, A. / Jin, Y. / Dregger, C. / Franklin, E. / Weisman, L.S. / Khan, A.R.
CitationJournal: Febs Lett. / Year: 2011
Title: The activation cycle of Rab GTPase Ypt32 reveals structural determinants of effector recruitment and GDI binding.
Authors: Sultana, A. / Jin, Y. / Dregger, C. / Franklin, E. / Weisman, L.S. / Khan, A.R.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GTP-binding protein YPT32/YPT11
A: GTP-binding protein YPT32/YPT11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1416
Polymers41,2062
Non-polymers9354
Water8,917495
1
B: GTP-binding protein YPT32/YPT11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0713
Polymers20,6031
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GTP-binding protein YPT32/YPT11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0713
Polymers20,6031
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-47 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.000, 45.200, 73.400
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE QUATERNARY STRUCTURE OF YPT32 IN SOLUTION IS A MONOMER. THE DIMER THAT WAS OBSERVED IN THE STRUCTURE IS A RESULT OF CRYSTALLOGRAPHIC PACKING.

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Components

#1: Protein GTP-binding protein YPT32/YPT11 / Rab GTPase YPT32


Mass: 20603.062 Da / Num. of mol.: 2 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YGL210W, YPT11, YPT32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P51996
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MGCL2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97849
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.7→68.75 Å / Num. obs: 44104 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.66 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0044refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CPJ

3cpj


Resolution: 1.7→68.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.362 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2223 5 %RANDOM
Rwork0.167 ---
obs0.169 44104 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0.08 Å2
2--0.15 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→68.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 58 495 3253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222907
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.973984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15925.035143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31615495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0071516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022208
X-RAY DIFFRACTIONr_mcbond_it0.7781.51757
X-RAY DIFFRACTIONr_mcangle_it1.41822847
X-RAY DIFFRACTIONr_scbond_it1.94431150
X-RAY DIFFRACTIONr_scangle_it3.0294.51115
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 156 -
Rwork0.242 3087 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3109-0.0817-0.28080.2973-0.1090.67860.02720.00940.00780.0045-0.0376-0.01980.03060.00480.01030.0243-0.0012-0.00810.0106-0.00980.03222.909-7.30345.407
21.8654-1.45321.51121.1672-1.331.9537-0.04870.15610.356-0.0007-0.1744-0.27570.01290.31390.22310.119-0.01890.0190.08480.01580.13069.892-9.74553.775
35.66581.4315-1.16330.8177-0.57480.45220.0368-0.4353-0.26960.178-0.1581-0.1692-0.02940.13360.12130.2305-0.0023-0.02610.1221-0.00680.096211.842-8.9641.586
40.60550.2993-0.34051.3292-0.76780.92890.05590.0557-0.0122-0.0096-0.0675-0.05670.0431-0.00070.01150.03750.0003-0.00350.0209-0.00970.03421.469-6.14844.427
53.0462-0.3546-0.0471.777-1.0431.0183-0.0340.1690.05070.06530.05710.07190.0135-0.2984-0.02320.0288-0.0293-0.00250.1721-0.00790.0805-6.454-4.55143.797
60.473-0.0334-0.2280.5493-0.17421.40150.04890.05920.00920.02060.00920.03570.0153-0.1935-0.05810.01010.0044-0.00960.0358-0.01150.0545-3.028-6.27244.462
70.5708-0.1182-0.09380.6250.10090.82950.04760.0265-0.00560.0226-0.0566-0.02990.0319-0.00880.0090.01020.0028-0.01190.0091-0.00890.03815.075-8.67345.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 35
2X-RAY DIFFRACTION1B10 - 35
3X-RAY DIFFRACTION2A36 - 47
4X-RAY DIFFRACTION3B36 - 47
5X-RAY DIFFRACTION4A48 - 68
6X-RAY DIFFRACTION4B48 - 68
7X-RAY DIFFRACTION5A69 - 78
8X-RAY DIFFRACTION5B69 - 78
9X-RAY DIFFRACTION6A79 - 112
10X-RAY DIFFRACTION6B79 - 112
11X-RAY DIFFRACTION7A121 - 178
12X-RAY DIFFRACTION7B121 - 178

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