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- PDB-4phg: Crystal structure of Ypt7 covalently modified with GTP -

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Basic information

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


RHOD GTPase cycle / TBC/RABGAPs / RHOQ GTPase cycle / RAB geranylgeranylation / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / 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 / TBC/RABGAPs / RHOQ GTPase cycle / RAB geranylgeranylation / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / protein localization to vacuole / cytoplasm to vacuole targeting by the Cvt pathway / fungal-type vacuole / piecemeal microautophagy of the nucleus / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / vacuole / regulation of protein-containing complex assembly / vesicle-mediated transport / Neutrophil degranulation / multivesicular body / macroautophagy / endocytosis / 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 / Rossmann fold ...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
Chem-2UJ / YTTRIUM (III) ION / Ypt/Rab-type GTPase YPT7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsKoch, D. / Wiegandt, D. / Vieweg, S. / Hofmann, F. / 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_symmetry / _struct_conn_type.id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein YPT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2266
Polymers20,2991
Non-polymers9275
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.970, 53.160, 46.910
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein YPT7


Mass: 20298.980 Da / Num. of mol.: 1 / Fragment: UNP residues 1-182 / Mutation: E35C, K38I, Q68L
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2UJ / N-[3-(propanoylamino)propyl]guanosine 5'-(tetrahydrogen triphosphate)


Mass: 636.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N6O15P3
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG3350, 0.2 M LiCl, 10mM Yttrium(III)-chlorid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.01 Å / Num. obs: 12310 / % possible obs: 99.5 % / Redundancy: 3.33 % / Rsym value: 0.07 / Net I/σ(I): 11.15
Reflection shellResolution: 1.9→2 Å / Rsym value: 0.362

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementResolution: 1.9→45.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.451 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 616 5 %RANDOM
Rwork0.17472 ---
obs0.17758 11694 99.58 %-
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: 26.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å22.57 Å2
2---0.29 Å20 Å2
3---1.85 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 44 52 1452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021427
X-RAY DIFFRACTIONr_bond_other_d0.0070.02920
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9791940
X-RAY DIFFRACTIONr_angle_other_deg1.2123.0112263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16325.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.671154
X-RAY DIFFRACTIONr_chiral_restr0.1560.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 43 -
Rwork0.231 840 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 11.9271 Å / Origin y: -5.5569 Å / Origin z: 11.6802 Å
111213212223313233
T0.0216 Å20.0016 Å20 Å2-0.0127 Å2-0.0034 Å2--0.012 Å2
L1.0369 °2-0.1002 °20.0519 °2-0.1882 °2-0.0472 °2--0.3511 °2
S0.0003 Å °-0.0517 Å °0.0124 Å °-0.0388 Å °0.019 Å °-0.0338 Å °0.011 Å °-0.036 Å °-0.0193 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 181
2X-RAY DIFFRACTION1A201 - 202

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