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- PDB-3idq: Crystal structure of S. cerevisiae Get3 at 3.7 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3idq
TitleCrystal structure of S. cerevisiae Get3 at 3.7 Angstrom resolution
ComponentsATPase GET3
KeywordsHYDROLASE / deviant Walker A motif / Arsenical resistance / ATP-binding / Cytoplasm / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Nucleotide-binding / Transport
Function / homology
Function and homology information


GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / response to heat / cellular response to oxidative stress / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.701 Å
AuthorsSuloway, C.J.M. / Chartron, J.W. / Zaslaver, M. / Clemons Jr., W.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Model for eukaryotic tail-anchored protein binding based on the structure of Get3
Authors: Suloway, C.J. / Chartron, J.W. / Zaslaver, M. / Clemons, W.M.
History
DepositionJul 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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
A: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2573
Polymers41,1331
Non-polymers1242
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATPase GET3
hetero molecules

A: ATPase GET3
hetero molecules

A: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7709
Polymers123,3983
Non-polymers3726
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4090 Å2
ΔGint-158 kcal/mol
Surface area40700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.320, 115.320, 281.111
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-370-

NI

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Components

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-translocating ATPase / Arsenical resistance ATPase / ...Arsenical pump-driving ATPase / Arsenite-translocating ATPase / Arsenical resistance ATPase / Arsenite-transporting ATPase / Golgi to ER traffic protein 3


Mass: 41132.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GET3, ARR4, YDL100C, D2371 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12154, EC: 3.6.3.16
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.37 Å3/Da / Density % sol: 71.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M HEPES, 1.6 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.701→47.054 Å / Num. obs: 7954 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rsym value: 0.099
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 6 % / Rsym value: 0.627 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data processing
PHENIX1.4_62refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IBG

1ibg


Resolution: 3.701→47.054 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.54 / σ(F): 1.34 / Stereochemistry target values: ML
Details: Residues designated 365-369 are part of the histidine tag used in purification. Density connecting these residues to the rest of the protein in chain A was not observed, therefore it is ...Details: Residues designated 365-369 are part of the histidine tag used in purification. Density connecting these residues to the rest of the protein in chain A was not observed, therefore it is possible they are extending from a symmetry related copy.
RfactorNum. reflection% reflectionSelection details
Rfree0.335 358 4.51 %RANDOM
Rwork0.283 ---
obs0.285 7936 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 401.21 Å2 / Biso mean: 182.045 Å2 / Biso min: 59 Å2
Baniso -1Baniso -2Baniso -3
1--33.786 Å2-0 Å20 Å2
2---33.786 Å2-0 Å2
3---65.133 Å2
Refinement stepCycle: LAST / Resolution: 3.701→47.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 2 0 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072222
X-RAY DIFFRACTIONf_angle_d1.1472990
X-RAY DIFFRACTIONf_chiral_restr0.08339
X-RAY DIFFRACTIONf_plane_restr0.004381
X-RAY DIFFRACTIONf_dihedral_angle_d23.6341349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.701-4.2360.3631150.3224812596100
4.236-5.3360.2811180.22725022620100
5.336-47.0570.3511250.2972595272099

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