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- PDB-3a36: Structural insight into the membrane insertion of tail-anchored p... -

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Basic information

Entry
Database: PDB / ID: 3a36
TitleStructural insight into the membrane insertion of tail-anchored proteins by Get3
ComponentsATPase GET3
KeywordsHYDROLASE / homo dimer / ATPase / zinc binding / 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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / 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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / cellular response to oxidative stress / response to heat / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYamagata, A. / Mimura, H. / Sato, Y. / Yamashita, M. / Yoshikawa, A. / Fukai, S.
CitationJournal: Genes Cells / Year: 2010
Title: Structural insight into the membrane insertion of tail-anchored proteins by Get3
Authors: Yamagata, A. / Mimura, H. / Sato, Y. / Yamashita, M. / Yoshikawa, A. / Fukai, S.
History
DepositionJun 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1113
Polymers81,0462
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-49 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.925, 221.639, 49.274
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ATPase GET3 / Arr4p / Golgi to ER traffic protein 3 / MEMBRANE PROTEIN INSERTION


Mass: 40522.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: NRRL Y-53 / Gene: 851458 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q12154, EC: 3.6.3.16
#2: 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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13.5% PEG 3350, 0.18M tri-sodium citrate, 9% MPD, 90mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 31955 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 63.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 38.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2937 / Rsym value: 0.263 / % possible all: 92.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 92769.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3117 10.1 %RANDOM
Rwork0.237 ---
obs0.237 30980 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.4287 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 79.9 Å2
Baniso -1Baniso -2Baniso -3
1--25.72 Å20 Å20 Å2
2--17.27 Å20 Å2
3---8.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 1 0 4897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 480 10.4 %
Rwork0.334 4148 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

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