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- PDB-4asw: Structure of the complex between the N-terminal dimerisation doma... -

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Basic information

Entry
Database: PDB / ID: 4asw
TitleStructure of the complex between the N-terminal dimerisation domain of Sgt2 and the UBL domain of Get5
Components
  • SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2
  • UBIQUITIN-LIKE PROTEIN MDY2
KeywordsCHAPERONE / TAIL-ANCHORED / POST-TRANSLATIONAL TARGETING
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / response to heat / protein-macromolecule adaptor activity / molecular adaptor activity / identical protein binding ...cell morphogenesis involved in conjugation with cellular fusion / TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / response to heat / protein-macromolecule adaptor activity / molecular adaptor activity / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Mdy2, Get4 binding domain / SGTA, homodimerisation domain / Get5, C-terminal domain / Homodimerisation domain of SGTA / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / : / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat ...Mdy2, Get4 binding domain / SGTA, homodimerisation domain / Get5, C-terminal domain / Homodimerisation domain of SGTA / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / : / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small glutamine-rich tetratricopeptide repeat-containing protein 2 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / ARIA
AuthorsSimon, A.C. / Simpson, P.J. / Goldstone, R.M. / Krysztofinska, E.M. / Murray, J.W. / High, S. / Isaacson, R.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the Sgt2/Get5 Complex Provides Insights Into Get-Mediated Targeting of Tail-Anchored Membrane Proteins
Authors: Simon, A.C. / Simpson, P.J. / Goldstone, R.M. / Krysztofinska, E.M. / Murray, J.W. / High, S. / Isaacson, R.L.
History
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Nov 30, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Revision 2.0Jun 23, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Other
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.name
Revision 2.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2
B: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2
C: UBIQUITIN-LIKE PROTEIN MDY2


Theoretical massNumber of molelcules
Total (without water)29,4623
Polymers29,4623
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 100LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2 / SGT2_NT / SGT/UBP / VIRAL PROTEIN U-BINDING PROTEIN


Mass: 10098.163 Da / Num. of mol.: 2 / Fragment: DIMERISATION DOMAIN, RESIDUES 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET46-SGT2_NT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q12118
#2: Protein UBIQUITIN-LIKE PROTEIN MDY2 / GOLGI TO ER TRAFFIC PROTEIN 5 / MATING-DEFICIENT PROTEIN 2 / TRANSLATION MACHINERY-ASSOCIATED ...GOLGI TO ER TRAFFIC PROTEIN 5 / MATING-DEFICIENT PROTEIN 2 / TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24 / GET5 / GET


Mass: 9265.789 Da / Num. of mol.: 1 / Fragment: RESIDUES 70-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET46-SGT2_NT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q12285

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111600
121800
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 250 mM / pH: 6 / Pressure: 1 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIBrukerAVANCE II8002

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Processing

NMR software
NameDeveloperClassification
ARIABARDIAUX B,MALLIAVIN T,NILGES Mrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1 / Details: BMRB 18342
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 9

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