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- PDB-2lxb: Solution structure of the Sgt2 homodimerization domain -

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Basic information

Entry
Database: PDB / ID: 2lxb
TitleSolution structure of the Sgt2 homodimerization domain
ComponentsSmall glutamine-rich tetratricopeptide repeat-containing protein 2
KeywordsPROTEIN BINDING / four-helix bundle / protein-protein interaction / Get5 binding domain / GET pathway
Function / homology
Function and homology information


TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to heat / molecular adaptor activity / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / 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 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChartron, J.W. / Vandervelde, D.G. / Clemons Jr., W.M.
CitationJournal: Cell Rep / Year: 2012
Title: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface.
Authors: Chartron, J.W. / Vandervelde, D.G. / Clemons, W.M.
History
DepositionAug 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)15,7792
Polymers15,7792
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Small glutamine-rich tetratricopeptide repeat-containing protein 2 / SGT/UBP / Viral protein U-binding protein


Mass: 7889.721 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SGT2, UNF346, YOR007C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: Q12118

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D 1H-15N TOCSY
1612D 1H-13C HSQC aliphatic
1713D 1H-15N NOESY
1813D HNCA
1913D HNCO
11013D C(CO)NH
11112D 1H-13C HSQC aromatic
11213D 1H-13C NOESY aromatic
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11532D 1H-15N HSQC
11622D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 13C; U-100% 15N] Sgt2, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-100% 15N] Sgt2, 20 mM sodium phosphate, 0.02 % sodium azide, 7 % Polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
32 mM [U-100% 15N] Sgt2, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMSgt2-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
0.02 %sodium azide-31
2 mMSgt2-4[U-100% 15N]2
20 mMsodium phosphate-52
0.02 %sodium azide-62
7 %Polyacrylamide-72
2 mMSgt2-8[U-100% 15N]3
20 mMsodium phosphate-93
0.02 %sodium azide-103
Sample conditionsIonic strength: 0 / pH: 6.1 / Pressure: ambient / Temperature: 297.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS+Cornilescu, Delaglio and Baxdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
PALESZweckstetter and Baxdata analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINED IN EXPLICIT WATER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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