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- PDB-3rwm: Crystal Structure of Ypt32 in Complex with GppNHp -

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Basic information

Entry
Database: PDB / ID: 3rwm
TitleCrystal Structure of Ypt32 in Complex with GppNHp
ComponentsGTP-binding protein YPT32/YPT11
KeywordsPROTEIN TRANSPORT / Ypt32 / Rab GTPase / vesicle trafficking / Effectors / Myo2p / GppNHp
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 ...: / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding protein YPT32/YPT11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSultana, A. / Dregger, C. / Jin, Y. / 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 1.3Feb 28, 2024Group: 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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,6724
Polymers20,6031
Non-polymers1,0693
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.090, 49.890, 90.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20603.062 Da / Num. of mol.: 1 / 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→45.33 Å / Num. obs: 14958 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.21 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.57
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0044refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.635 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 757 5.1 %RANDOM
Rwork0.194 ---
obs0.196 14958 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.928 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å20 Å2
2--1.57 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 65 192 1672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg2.014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.081
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.262
X-RAY DIFFRACTIONr_chiral_restr0.207
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_mcbond_it0.487
X-RAY DIFFRACTIONr_mcangle_it0.871
X-RAY DIFFRACTIONr_scbond_it1.367
X-RAY DIFFRACTIONr_scangle_it2.109
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 52 -
Rwork0.254 1039 -
obs--100 %
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)
10.0849-0.9314-0.195511.79972.46880.51670.0245-0.02650.01320.0761-0.0242-0.02510.0164-0.0037-0.00030.0878-0.04920.02850.0817-0.03090.0426-5.338718.26428.3309
24.42980.1457-1.3110.6758-0.08281.64860.1082-0.36480.16660.0496-0.194-0.0397-0.26020.32570.08580.059-0.0594-0.0180.1150.01490.03979.66814.641114.861
37.98820.43882.90493.42121.12422.29160.214-0.20630.9172-0.1198-0.252-0.0295-0.44210.35620.0380.2994-0.23990.12340.317-0.11550.287416.177423.7199.7506
46.8921-0.0675-3.60991.6771-0.48184.14380.2277-0.61970.29090.2258-0.1960.2342-0.22220.1705-0.03170.099-0.05090.00880.1031-0.07160.07882.338414.923120.2179
53.99621.817-5.66121.1801-3.864312.73040-0.4858-0.17140.0745-0.182-0.0682-0.25490.49920.18190.0668-0.0548-0.05390.30210.13620.081223.568110.088923.2501
63.68420.2774-3.4270.63160.15363.4669-0.0473-0.4959-0.2375-0.0298-0.1141-0.11740.02250.41990.16140.0236-0.0141-0.01240.13980.09280.068614.34597.828213.8111
73.79641.1298-2.94540.411-0.65047.6057-0.1981-0.6099-0.6379-0.0902-0.1477-0.12680.40170.54640.34580.09720.05990.01310.17940.1730.2118.31111.213614.6627
82.26881.062-1.36184.5954-4.18794.54240.01040.132-0.11230.04390.0510.0217-0.12270.0348-0.06140.022-0.01540.00640.06280.01050.038411.37110.30833.2095
94.14472.6076-5.63264.1493-3.43818.6037-0.62370.2639-0.7412-0.44060.0338-0.28750.8629-0.08730.58990.1176-0.04160.06850.1431-0.13050.387512.60130.27460.722
102.5583-0.0639-0.70230.297-0.06541.3929-0.1110.0096-0.1413-0.0972-0.05820.05860.0748-0.06510.16930.06170.00460.00050.0411-0.00570.07082.81489.20668.5922
1112.436111.47020.260910.79870.68951.1236-0.20710.64360.3171-0.33290.38630.1981-0.4207-0.2858-0.17920.18010.07710.03380.2730.10030.0731-9.864-1.451221.6054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B6 - 11
2X-RAY DIFFRACTION2B12 - 35
3X-RAY DIFFRACTION3B36 - 47
4X-RAY DIFFRACTION4B48 - 70
5X-RAY DIFFRACTION5B71 - 81
6X-RAY DIFFRACTION6B82 - 97
7X-RAY DIFFRACTION7B98 - 119
8X-RAY DIFFRACTION8B120 - 131
9X-RAY DIFFRACTION9B132 - 149
10X-RAY DIFFRACTION10B150 - 175
11X-RAY DIFFRACTION11B176 - 184

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