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- PDB-2lxc: Solution structure of the complex between the Sgt2 homodimerizati... -

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Basic information

Entry
Database: PDB / ID: 2lxc
TitleSolution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain
Components
  • Small glutamine-rich tetratricopeptide repeat-containing protein 2
  • Ubiquitin-like protein MDY2
KeywordsPROTEIN BINDING/PROTEIN BINDING / ubiquitin-like domain / protein-protein interaction / four-helix bundle / GET pathway / PROTEIN BINDING-PROTEIN BINDING complex
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRC complex / tail-anchored membrane protein insertion into ER membrane / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / protein-folding chaperone binding / response to heat / molecular adaptor activity ...cell morphogenesis involved in conjugation with cellular fusion / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRC complex / tail-anchored membrane protein insertion into ER membrane / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / protein-folding chaperone binding / response to heat / molecular adaptor activity / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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 / SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...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 / SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeats / 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 / simulated annealing, experimentally driven docking
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: Ubiquitin-like protein MDY2
B: Small glutamine-rich tetratricopeptide repeat-containing protein 2
C: Small glutamine-rich tetratricopeptide repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)24,9503
Polymers24,9503
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like protein MDY2 / Golgi to ER traffic protein 5 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 9170.796 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET5, MDY2, TMA24, YOL111C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: Q12285
#2: 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 1H-15N NOESY
1313D 1H-15N TOCSY
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1632D 1H-15N HSQC
1733D HN(CA)CB
1833D HNCO
1933D (H)CCH-TOCSY
11033D (H)CCH-TOCSY
11133D 1H-15N NOESY
11233D 1H-13C NOESY aliphatic
11322D 1H-15N HSQC
11442D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGet5-11
2 mMSgt2-2[U-100% 13C; U-100% 15N]1
10 mMBis-Tris-31
50 mML-arginine-41
50 mML-glutamic acid-51
0.02 %sodium azide-61
1 mMGet5-72
2 mMSgt2-8[U-100% 13C; U-100% 15N]2
10 mMBis-Tris-92
50 mML-arginine-102
50 mML-glutamic acid-112
0.02 %sodium azide-122
3.5 %polyacrylamide-132
1 mMGet5-14[U-100% 13C; U-100% 15N]3
2 mMSgt2-153
10 mMBis-Tris-163
50 mML-arginine-173
50 mML-glutamic acid-183
0.02 %sodium azide-193
1 mMGet5-20[U-100% 13C; U-100% 15N]4
2 mMSgt2-214
10 mMBis-Tris-224
50 mML-arginine-234
50 mML-glutamic acid-244
0.02 %sodium azide-254
3.5 %polyacrylamide-264
Sample conditionsIonic strength: 0 / pH: 6.1 / Pressure: ambient / Temperature: 310 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
HADDOCK2.1Alexandre Bonvinstructure solution
TopSpinBruker Biospincollection
PALESZweckstetter and Baxdata analysis
RefinementMethod: simulated annealing, experimentally driven docking / Software ordinal: 1
Details: STRUCTURES OF ASYMMETRICALLY LABELED COMPLEX (SAMPLE_1 AND SAMPLE_3) WERE USED TO DETERMINE THE SEPERATE STRUCTURES OF GET5 OR SGT2, IN THEIR COMPLEX STATES. STRUCTURES ARE REFINED IN ...Details: STRUCTURES OF ASYMMETRICALLY LABELED COMPLEX (SAMPLE_1 AND SAMPLE_3) WERE USED TO DETERMINE THE SEPERATE STRUCTURES OF GET5 OR SGT2, IN THEIR COMPLEX STATES. STRUCTURES ARE REFINED IN EXPLICIT WATER. AMBIGUOUS INTERACTION RESTRAINTS, RESIDUAL DIPOLAR COUPLINGS AND INTERMOLECULAR NOES WERE USED TO DOCK THE STRUCTURES OF GET5 AND SGT2, DETERMINED IN THEIR COMPLEX STATES. STRUCTURES ARE SELECTED FROM THE BEST SCORING CLUSTER BY HADDOCK SCORES AND REFINED IN WATER.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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