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- PDB-4pwx: Crystal structure of an ATP-bound Get3-Get4-Get5 complex from S.c... -

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Basic information

Entry
Database: PDB / ID: 4pwx
TitleCrystal structure of an ATP-bound Get3-Get4-Get5 complex from S.cerevisiae
Components
  • ATPase GET3
  • Golgi to ER traffic protein 4
  • Ubiquitin-like protein MDY2
KeywordsTRANSPORT PROTEIN / Tail-anchored targeting
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC 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 ...cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC 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 / vesicle-mediated transport / protein folding chaperone / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / unfolded protein binding / protein-macromolecule adaptor activity / cellular response to oxidative stress / response to heat / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Golgi to ER traffic protein 4 / ATPase GET3 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.4 Å
AuthorsGristick, H.B. / Clemons Jr., W.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal structure of ATP-bound Get3-Get4-Get5 complex reveals regulation of Get3 by Get4.
Authors: Gristick, H.B. / Rao, M. / Chartron, J.W. / Rome, M.E. / Shan, S.O. / Clemons, W.M.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id / _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
B: ATPase GET3
E: Golgi to ER traffic protein 4
F: Ubiquitin-like protein MDY2
C: Golgi to ER traffic protein 4
D: Ubiquitin-like protein MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,90411
Polymers158,7766
Non-polymers1,1285
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.341, 134.501, 84.060
Angle α, β, γ (deg.)90.00, 113.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 6 molecules ABECFD

#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: 39547.738 Da / Num. of mol.: 2 / Fragment: UNP residues 2-354 / Mutation: D57V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARR4, D2371, GET3, Get3 YDL100C, YDL100C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3)
References: UniProt: Q12154, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 4 / Guided entry of tail-anchored proteins 4


Mass: 33806.137 Da / Num. of mol.: 2 / Fragment: UNP residues 11-290 / Mutation: K258A, K260A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET4, GET4 YOR164C, O3580, YOR164C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q12125
#3: Protein Ubiquitin-like protein MDY2 / Golgi to ER traffic protein 5 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 6034.042 Da / Num. of mol.: 2 / Fragment: UNP residues 1-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET5, GET5 MDY2 YOL111C, MDY2, TMA24, YOL111C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q12285

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 18% PEG 3350, 0.2M potassium thiocyanate, 0.1M bis-tris propane, 5% DMSO, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
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: 5.4→30 Å / Num. all: 5529 / Num. obs: 5529 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.05
Reflection shellResolution: 5.4→6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / Num. unique all: 1597 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
Web-Icedata collection
PHASERphasing
REFMACv6.3refinement
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WOJ AND 3LKU

2woj

3lku


Resolution: 5.4→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.328 537 Random
Rwork0.27 --
all-5529 -
obs-4992 -
Refinement stepCycle: LAST / Resolution: 5.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10094 0 65 0 10159

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