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- PDB-3vlc: Crystal structure of S. cerevisiae Get3 in the semi open conforma... -

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Basic information

Entry
Database: PDB / ID: 3vlc
TitleCrystal structure of S. cerevisiae Get3 in the semi open conformation in complex with Get1 cytosolic domain at 4.5 angstrom resolution
Components
  • ATPase GET3
  • Golgi to ER traffic protein 1
KeywordsHYDROLASE/TRANSPORT PROTEIN / ATPase / membrane protein insertion / ATP binding / membrane protein binding / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


pheromone-dependent signal transduction involved in conjugation with cellular fusion / GET complex / 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 / mitophagy ...pheromone-dependent signal transduction involved in conjugation with cellular fusion / GET complex / 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 / mitophagy / protein folding chaperone / protein-membrane adaptor activity / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Get 1, fungi / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Golgi to ER traffic protein 1 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsKubota, K. / Yamagata, A. / Fukai, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces
Authors: Kubota, K. / Yamagata, A. / Sato, Y. / Goto-Ito, S. / Fukai, S.
History
DepositionNov 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: ATPase GET3
E: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1343
Polymers50,7072
Non-polymers4271
Water0
1
A: ATPase GET3
E: Golgi to ER traffic protein 1
hetero molecules

A: ATPase GET3
E: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2696
Polymers101,4154
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area29420 Å2
Unit cell
Length a, b, c (Å)132.634, 132.634, 185.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided ...Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided entry of tail-anchored proteins 3


Mass: 39451.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: NRRL Y-53 / Plasmid: PETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q12154*PLUS, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 1 / Guided entry of tail-anchored proteins 1 / Mitochondrial distribution and morphology protein 39


Mass: 11255.633 Da / Num. of mol.: 1 / Fragment: UNP residues 21-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET1, MDM39, YGL020C / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P53192
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR ENTITY 1 (CHAIN A) WHICH DERIVES FROM STRAIN NRRL Y-53 DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR ENTITY 1 (CHAIN A) WHICH DERIVES FROM STRAIN NRRL Y-53 DOES NOT CURRENTLY EXIST.

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 13.5% PEG 3350, 0.18M trisodium citrate, 9% MPD, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 3862 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rsym value: 0.05 / Net I/σ(I): 45.8
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 191 / Rsym value: 0.313 / % possible all: 98.5

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B2E

3b2e


Resolution: 4.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3659 201 5.2 %RANDOM
Rwork0.3457 ---
all-3879 --
obs-3843 --
Solvent computationBsol: 113.826 Å2
Displacement parametersBiso max: 268.89 Å2 / Biso mean: 220.9105 Å2 / Biso min: 168.36 Å2
Baniso -1Baniso -2Baniso -3
1-23.164 Å20 Å20 Å2
2--23.164 Å20 Å2
3----46.328 Å2
Refinement stepCycle: LAST / Resolution: 4.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 27 0 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.396
X-RAY DIFFRACTIONc_mcbond_it1.1931.5
X-RAY DIFFRACTIONc_scbond_it1.0382
X-RAY DIFFRACTIONc_mcangle_it2.2142
X-RAY DIFFRACTIONc_scangle_it1.922.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6ADP.param

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