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- PDB-2lnz: Solution structure of the Get5 carboxyl domain from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2lnz
TitleSolution structure of the Get5 carboxyl domain from S. cerevisiae
ComponentsUbiquitin-like protein MDY2
KeywordsPROTEIN BINDING / dimerization / homodimerization
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / 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 / nucleus / cytosol / cytoplasm
Similarity search - Function
Get5 dimerization domain / 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 / GTP Cyclohydrolase I; Chain A, domain 1 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Get5 dimerization domain / 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 / GTP Cyclohydrolase I; Chain A, domain 1 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons Jr., W.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Get5 Carboxyl-terminal Domain Is a Novel Dimerization Motif That Tethers an Extended Get4/Get5 Complex.
Authors: Chartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons, W.M.
History
DepositionJan 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.3May 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: Ubiquitin-like protein MDY2


Theoretical massNumber of molelcules
Total (without water)14,2482
Polymers14,2482
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 Ubiquitin-like protein MDY2 / Golgi to ER traffic protein 5 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 7123.891 Da / Num. of mol.: 2 / Fragment: carboxyl domain residues 152-212
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12285

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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 C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1912D 1H-13C HSQC
11012D 1H-13C HSQC aromatic
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-15N TOCSY
11413D HBHA(CO)NH
11513D H(CCO)NH
11632D 1H-15N HSQC
11722D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5 mM [U-100% 13C; U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
22.5 mM [U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 4 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
32.5 mM [U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.5 mMGet5-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
0.02 %sodium azide-31
2.5 mMGet5-4[U-100% 15N]2
20 mMsodium phosphate-52
0.02 %sodium azide-62
4 %polyacrylamide-72
2.5 mMGet5-8[U-100% 15N]3
20 mMsodium phosphate-93
0.02 %sodium azide-103
Sample conditionsIonic strength: 50 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
REDCATPrestegarddata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: log-harmonic potential used
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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