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- PDB-4phh: Crystal structure of Ypt7 covalently modified with GNP -

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Basic information

Entry
Database: PDB / ID: 4phh
TitleCrystal structure of Ypt7 covalently modified with GNP
ComponentsGTP-binding protein YPT7
KeywordsEndocytosis / exocytosis / Ypt7 / acryl-nucleotides / aGNP / covalent / GNP / GppNHp
Function / homology
Function and homology information


RHOD GTPase cycle / RHOQ GTPase cycle / TBC/RABGAPs / RAB geranylgeranylation / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / protein localization to vacuole / cytoplasm to vacuole targeting by the Cvt pathway ...RHOD GTPase cycle / RHOQ GTPase cycle / TBC/RABGAPs / RAB geranylgeranylation / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / protein localization to vacuole / cytoplasm to vacuole targeting by the Cvt pathway / piecemeal microautophagy of the nucleus / fungal-type vacuole / fungal-type vacuole membrane / vacuole / retrograde transport, endosome to Golgi / regulation of protein-containing complex assembly / phagocytic vesicle / vesicle-mediated transport / Neutrophil degranulation / macroautophagy / endocytosis / protein transport / late endosome / mitochondrial outer membrane / GTPase activity / protein-containing complex binding / GTP binding / mitochondrion / 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
Chem-2UK / Ypt/Rab-type GTPase YPT7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsWiegandt, D. / Vieweg, S. / Hofmann, F. / Koch, D. / Wu, Y. / Itzen, A. / Mueller, M.P. / Goody, R.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB642, grant A4 Germany
German Research Foundation (DFG)SFB1035, project B05 Germany
CitationJournal: Nat Commun / Year: 2015
Title: Locking GTPases covalently in their functional states.
Authors: Wiegandt, D. / Vieweg, S. / Hofmann, F. / Koch, D. / Li, F. / Wu, Y.W. / Itzen, A. / Muller, M.P. / Goody, R.S.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein YPT7
B: GTP-binding protein YPT7
C: GTP-binding protein YPT7
D: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,06515
Polymers81,3204
Non-polymers2,74511
Water30617
1
A: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0254
Polymers20,3301
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0254
Polymers20,3301
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9903
Polymers20,3301
Non-polymers6602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0254
Polymers20,3301
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 72.230, 82.340
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GTP-binding protein YPT7


Mass: 20329.973 Da / Num. of mol.: 4 / Fragment: UNP residues 1-182 / Mutation: Q35C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: YPT7, VAM4, YML001W, YM8270.02 / Production host: Escherichia coli (E. coli) / References: UniProt: P32939
#2: Chemical
ChemComp-2UK / 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-N-[3-(propanoylamino)propyl]guanosine


Mass: 635.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H28N7O14P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris pH 7, 25 % PEG 6000, 1 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.92045 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92045 Å / Relative weight: 1
ReflectionResolution: 2.35→48.18 Å / Num. obs: 29719 / % possible obs: 99.9 % / Redundancy: 6.88 % / Rsym value: 0.058 / Net I/σ(I): 18.28
Reflection shellResolution: 2.35→2.45 Å / Rsym value: 0.555

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementResolution: 2.35→48.18 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.472 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26301 1486 5 %RANDOM
Rwork0.20008 ---
obs0.20331 28232 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.921 Å2
Baniso -1Baniso -2Baniso -3
1--7.55 Å20 Å20.26 Å2
2--6.2 Å20 Å2
3---1.36 Å2
Refinement stepCycle: 1 / Resolution: 2.35→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 167 17 5337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025406
X-RAY DIFFRACTIONr_bond_other_d0.0040.023447
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9767346
X-RAY DIFFRACTIONr_angle_other_deg1.1053.0128462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48925.714231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551515
X-RAY DIFFRACTIONr_chiral_restr0.120.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 104 -
Rwork0.292 2006 -
obs--99.81 %
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)
18.3993-0.1186-2.19613.48120.60113.1563-0.2684-0.2666-0.0212-0.02720.1121-0.08090.14940.34030.15630.19510.0275-0.04330.28390.0380.046337.3645-13.743844.0305
210.3246-1.4213-0.40933.497-0.11395.6132-0.24610.58820.298-0.3054-0.3847-0.76150.04530.13440.63080.2590.02180.04710.06570.10730.360548.1937-5.80182.2689
38.672-0.23950.19383.39660.0512.8803-0.02580.3230.4667-0.1929-0.212-0.5348-0.1780.42460.23780.249-0.0033-0.00270.31090.10320.223251.833724.759526.6479
49.25520.9151-0.57314.1492-0.64944.36970.1365-0.53740.61510.1791-0.06220.30020.0431-0.0796-0.07430.2002-0.0089-0.04440.0434-0.05560.115318.0758-5.692613.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 181
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B8 - 182
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C8 - 182
6X-RAY DIFFRACTION3C201 - 202
7X-RAY DIFFRACTION4D7 - 182
8X-RAY DIFFRACTION4D201 - 202

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