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- PDB-3b2e: Crystal structure of S. cerevisiae Get3 in the open conformation ... -

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Basic information

Entry
Database: PDB / ID: 3b2e
TitleCrystal structure of S. cerevisiae Get3 in the open conformation in complex with Get1 cytosolic domain
Components
  • ATPase GET3
  • Golgi to ER traffic protein 1
KeywordsHYDROLASE/TRANSPORT PROTEIN / Protein-protein interaction / receptor complex / HYDROLASE / TRANSPORT PROTEIN / ADP binding / Coild-coil / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum membrane / 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 ...establishment of protein localization to endoplasmic reticulum membrane / 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 transmembrane transporter activity / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / response to heat / cellular response to oxidative stress / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Get 1, fungi / Helix hairpin bin / 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 / Helix Hairpins ...Get 1, fungi / Helix hairpin bin / 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 / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 3 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
DepositionJul 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: ATPase GET3
F: Golgi to ER traffic protein 1
C: ATPase GET3
G: Golgi to ER traffic protein 1
D: ATPase GET3
H: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,05712
Polymers202,3488
Non-polymers1,7094
Water00
1
A: ATPase GET3
E: Golgi to ER traffic protein 1
B: ATPase GET3
F: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0296
Polymers101,1744
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATPase GET3
G: Golgi to ER traffic protein 1
D: ATPase GET3
H: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0296
Polymers101,1744
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.338, 167.663, 244.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
ATPase GET3


Mass: 40522.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: NRRL Y-53 / Plasmid: PETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q12154*PLUS, EC: 3.6.3.16
#2: Protein
Golgi to ER traffic protein 1 / Guided entry of tail-anchored proteins 1 / Mitochondrial distribution and morphology protein 39


Mass: 10064.349 Da / Num. of mol.: 4 / Fragment: Get1 cytosolic domain, UNP residues 20-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET1 / Plasmid: PETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P53192
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN A, B, C, D WHICH DERIVES FROM STRAIN NRRL Y-53 DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR CHAIN A, B, C, D 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 13.5% PEG3350, 0.18 M tri-sodium citrate, 9% MPD, 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 MX225HE / Detector: CCD / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 44560 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.1
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / % possible all: 87.2

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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: 3A36

3a36


Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.306 2231 RANDOM
Rwork0.274 --
all-44435 -
obs-44435 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12038 0 108 0 12146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.45

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