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- PDB-4cpg: Solution structure of the SGTA N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4cpg
TitleSolution structure of the SGTA N-terminal domain
ComponentsSMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN ALPHA
KeywordsCHAPERONE / SGTA / TAIL-ANCHORED / GET PATHWAY / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of ERAD pathway / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ERAD pathway / negative regulation of ubiquitin-dependent protein catabolic process ...negative regulation of ERAD pathway / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ERAD pathway / negative regulation of ubiquitin-dependent protein catabolic process / : / molecular adaptor activity / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Small glutamine-rich tetratricopeptide repeat-containing protein alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsDarby, J.F. / Krysztofinska, E.M. / Simpson, P.J. / Isaacson, R.L.
CitationJournal: Plos One / Year: 2014
Title: Solution Structure of the Sgta Dimerisation Domain and Investigation of its Interactions with the Ubiquitin-Like Domains of Bag6 and Ubl4A.
Authors: Darby, J.F. / Krysztofinska, E.M. / Simpson, P.J. / Simon, A.C. / Leznicki, P. / Sriskandarajah, N. / Bishop, D.S. / Hale, L.R. / Alfano, C. / Conte, M.R. / Martinez-Lumbreras, S. / ...Authors: Darby, J.F. / Krysztofinska, E.M. / Simpson, P.J. / Simon, A.C. / Leznicki, P. / Sriskandarajah, N. / Bishop, D.S. / Hale, L.R. / Alfano, C. / Conte, M.R. / Martinez-Lumbreras, S. / Thapaliya, A. / High, S. / Isaacson, R.L.
History
DepositionFeb 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.year / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.manufacturer
Revision 2.0Feb 14, 2018Group: Atomic model / Data collection / Category: atom_site / 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_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.1May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

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Assembly

Deposited unit
A: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN ALPHA
B: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN ALPHA


Theoretical massNumber of molelcules
Total (without water)18,4872
Polymers18,4872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN ALPHA / ALPHA-SGT / VPU-BINDING PROTEIN / UBP


Mass: 9243.259 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-69
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL DIMERISATION DOMAIN OF SGTA / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET46 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O43765

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1613D HBHA(CO)NH
1713D H(CCCO)NH
1813D (H)CC(CO)NH
1913D 1H-15N NOESY
11013D (H)CCH-TOCSY
11113D (H)CCH-TOCSY
11213D 1H-13C NOESY
11313D F1 1H(13C
114115N)-REJECT 13C NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED DIMERIC SGTA_NT

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Sample preparation

Details
Solution-IDContents
190% H2O/10% D2O
2100% D2O
Sample conditionsIonic strength: 250 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Home-built9502
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE8004
Bruker AVANCEBrukerAVANCE7005

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Processing

NMR software
NameDeveloperClassification
CNSA.T.BRUNGER,P.D.ADAMS,G.M.CLORE,W.L. DELANO,P.GROS, R.W.GROSSE-KUNSTLEVE,J.-S. JIANG,J.KUSZEWSKI, M.NILGES,N.S.PANNU,R.J. READ,L.M.RICE,T.SIMONSON,G.L.WARRENrefinement
NMRViewstructure solution
TALOSstructure solution
ARIAstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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