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- PDB-2lck: Structure of the mitochondrial uncoupling protein 2 determined by... -

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Basic information

Entry
Database: PDB / ID: 2lck
TitleStructure of the mitochondrial uncoupling protein 2 determined by NMR molecular fragment replacement
ComponentsMitochondrial uncoupling protein 2
KeywordsTRANSPORT PROTEIN / membrane protein / proton translocator / mitochondrial carrier / Structural Genomics / Membrane Protein Structures by Solution NMR / MPSbyNMR / PSI-Biology
Function / homology
Function and homology information


oxaloacetate transmembrane transporter activity / The fatty acid cycling model / phosphate ion uniporter activity / malate transmembrane transporter activity / negative regulation of calcium import into the mitochondrion / C4-dicarboxylate transport / cellular response to lead ion / mitochondrial transmembrane transport / secondary active sulfate transmembrane transporter activity / L-aspartate transmembrane transporter activity ...oxaloacetate transmembrane transporter activity / The fatty acid cycling model / phosphate ion uniporter activity / malate transmembrane transporter activity / negative regulation of calcium import into the mitochondrion / C4-dicarboxylate transport / cellular response to lead ion / mitochondrial transmembrane transport / secondary active sulfate transmembrane transporter activity / L-aspartate transmembrane transporter activity / response to fatty acid / response to superoxide / glutamine metabolic process / negative regulation of insulin secretion involved in cellular response to glucose stimulus / mitochondrial fission / chloride transmembrane transporter activity / antiporter activity / response to dexamethasone / proton transmembrane transporter activity / macrophage differentiation / long-chain fatty acid transport / liver regeneration / reactive oxygen species metabolic process / cellular response to amino acid starvation / glycolytic process / regulation of mitochondrial membrane potential / cellular response to glucose stimulus / mitochondrial membrane / cellular response to insulin stimulus / GDP binding / positive regulation of cold-induced thermogenesis / negative regulation of neuron apoptotic process / response to hypoxia / mitochondrial inner membrane / protein homodimerization activity / mitochondrion
Similarity search - Function
Mitochondrial carrier fold / Mitochondrial carrier domain / : / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Dicarboxylate carrier UCP2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / RDC-based Molecular Fragment Replacement, simulated annealing
Model detailslowest energy, model 1
AuthorsBerardi, M.J. / Chou, J.J. / Membrane Protein Structures by Solution NMR (MPSbyNMR)
CitationJournal: Nature / Year: 2011
Title: Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching.
Authors: Berardi, M.J. / Shih, W.M. / Harrison, S.C. / Chou, J.J.
History
DepositionApr 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial uncoupling protein 2


Theoretical massNumber of molelcules
Total (without water)33,0561
Polymers33,0561
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)15 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitochondrial uncoupling protein 2 / UCP 2 / Solute carrier family 25 member 8 / UCPH


Mass: 33056.074 Da / Num. of mol.: 1 / Fragment: sequence database residues 14-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ucp2, Slc25a8 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3 / References: UniProt: P70406

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY-HSQC
1213D TROSY-HNCA
1313D TROSY-HN(CO)CA
1413D TROSY-HN(CA)CB
1513D TROSY-HN(CO)CACB
1613D TROSY-HN(CA)CO
1713D TROSY-HNCO
1813D (HN,HN)-HMQC-NOESY-TROSY
1913D J(NH)-scaled TROSY-HNCO
11023D J(NH)-scaled TROSY-HNCO
11113D quantitative J(C'Ca) TROSY-HNCO
11223D quantitative J(C'Ca) TROSY-HNCO
11313D quantitative J(C'N) TROSY-HNCO
11423D quantitative J(C'N) TROSY-HNCO
11533D TROSY-HNCO
11643D TROSY-HNCO
11753D TROSY-HNCO
11863D TROSY-HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 2 w/v DNA nanotube, 95% H2O/5% D2O95% H2O/5% D2O
30.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2-SL1, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2-SL2, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
50.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2-SL3, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
60.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] UCP2-SL4, 5 mM guanosine diphosphate, 150 mM dodecylphosphocholine, 1 mM cardiolipin, 2 mM dimyristoyl-phosphatidylcholine, 5 mM beta-mercatpoethanol, 30 mM potassium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMUCP2-1[U-100% 13C; U-100% 15N; U-80% 2H]1
5 mMguanosine diphosphate-21
150 mMdodecylphosphocholine-31
1 mMcardiolipin-41
2 mMdimyristoyl-phosphatidylcholine-51
5 mMbeta-mercatpoethanol-61
30 mMpotassium phosphate-71
80 mMsodium chloride-81
0.5 mMUCP2-9[U-100% 13C; U-100% 15N; U-80% 2H]2
5 mMguanosine diphosphate-102
150 mMdodecylphosphocholine-112
1 mMcardiolipin-122
2 mMdimyristoyl-phosphatidylcholine-132
5 mMbeta-mercatpoethanol-142
30 mMpotassium phosphate-152
80 mMsodium chloride-162
2 w/vDNA nanotube-172
0.8 mMUCP2-SL1-18[U-100% 13C; U-100% 15N; U-80% 2H]3
5 mMguanosine diphosphate-193
150 mMdodecylphosphocholine-203
1 mMcardiolipin-213
2 mMdimyristoyl-phosphatidylcholine-223
5 mMbeta-mercatpoethanol-233
30 mMpotassium phosphate-243
80 mMsodium chloride-253
0.8 mMUCP2-SL2-26[U-100% 13C; U-100% 15N; U-80% 2H]4
5 mMguanosine diphosphate-274
150 mMdodecylphosphocholine-284
1 mMcardiolipin-294
2 mMdimyristoyl-phosphatidylcholine-304
5 mMbeta-mercatpoethanol-314
30 mMpotassium phosphate-324
80 mMsodium chloride-334
0.8 mMUCP2-SL3-34[U-100% 13C; U-100% 15N; U-80% 2H]5
5 mMguanosine diphosphate-355
150 mMdodecylphosphocholine-365
1 mMcardiolipin-375
2 mMdimyristoyl-phosphatidylcholine-385
5 mMbeta-mercatpoethanol-395
30 mMpotassium phosphate-405
80 mMsodium chloride-415
0.8 mMUCP2-SL4-42[U-100% 13C; U-100% 15N; U-80% 2H]6
5 mMguanosine diphosphate-436
150 mMdodecylphosphocholine-446
1 mMcardiolipin-456
2 mMdimyristoyl-phosphatidylcholine-466
5 mMbeta-mercatpoethanol-476
30 mMpotassium phosphate-486
80 mMsodium chloride-496
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 33 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XEASYBartels et al.chemical shift assignment
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
In_house_python_scriptrefinement
RefinementMethod: RDC-based Molecular Fragment Replacement, simulated annealing
Software ordinal: 1
Details: determining local structural segments by RDC-based MFR protocol, determining the spatial arrangement of the MFR-derived segments using PRE distance restraints
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 227 / Protein psi angle constraints total count: 227
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15
NMR ensemble rmsDistance rms dev: 0.041 Å

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