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- PDB-2n02: Solution structure of the A147T variant of the mitochondrial tran... -

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Basic information

Entry
Database: PDB / ID: 2n02
TitleSolution structure of the A147T variant of the mitochondrial translocator protein (tspo) in complex with pk11195
ComponentsTranslocator protein
KeywordsMEMBRANE PROTEIN / TRANSLOCATOR PROTEIN (TSPO) / PROTEIN-LIGAND COMPLEX / MITOCHONDRIA / PK11195 / PERIPHERAL BENZODIAZEPINE RECEPTOR / A147T
Function / homology
Function and homology information


negative regulation of corticosterone secretion / Pregnenolone biosynthesis / negative regulation of ATP metabolic process / response to vitamin B1 / peripheral nervous system axon regeneration / maintenance of protein location in mitochondrion / regulation of steroid biosynthetic process / benzodiazepine receptor activity / contact inhibition / establishment of protein localization to mitochondrion ...negative regulation of corticosterone secretion / Pregnenolone biosynthesis / negative regulation of ATP metabolic process / response to vitamin B1 / peripheral nervous system axon regeneration / maintenance of protein location in mitochondrion / regulation of steroid biosynthetic process / benzodiazepine receptor activity / contact inhibition / establishment of protein localization to mitochondrion / : / glial cell migration / response to acetylcholine / cellular hypotonic response / androgen binding / negative regulation of nitric oxide biosynthetic process / steroid biosynthetic process / positive regulation of calcium ion transport / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / chloride transport / response to manganese ion / cholesterol binding / cellular response to zinc ion / lipid transport / negative regulation of glial cell proliferation / positive regulation of mitochondrial depolarization / adrenal gland development / response to testosterone / behavioral response to pain / negative regulation of tumor necrosis factor production / monoatomic ion transport / positive regulation of glial cell proliferation / negative regulation of protein ubiquitination / cholesterol homeostasis / response to progesterone / positive regulation of reactive oxygen species metabolic process / cellular response to lipopolysaccharide / mitochondrial outer membrane / transmembrane transporter binding / response to xenobiotic stimulus / positive regulation of apoptotic process / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / cytosol
Similarity search - Function
TspO/MBR protein / TspO/MBR-related protein / TspO/MBR-related superfamily / TspO/MBR family / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PKA / Translocator protein / Translocator protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsJaremko, M. / Jaremko, L. / Giller, K. / Becker, S. / Zweckstetter, M.
CitationJournal: Chembiochem / Year: 2015
Title: Structural Integrity of the A147T Polymorph of Mammalian TSPO.
Authors: Jaremko, M. / Jaremko, M. / Giller, K. / Becker, S. / Zweckstetter, M.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translocator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1822
Polymers18,8291
Non-polymers3531
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 105structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translocator protein /


Mass: 18828.709 Da / Num. of mol.: 1 / Mutation: A147T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bzrp, Tspo / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q99M32, UniProt: P50637*PLUS
#2: Chemical ChemComp-PKA / N-[(2R)-butan-2-yl]-1-(2-chlorophenyl)-N-methylisoquinoline-3-carboxamide


Mass: 352.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21ClN2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CO)CA
1933D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aromatic
11313D HN(CA)CB
11433D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.7 mM [U-100% 13C; U-100% 15N] TRANSLOCATOR PROTEIN A147T, 0.3-0.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] TRANSLOCATOR PROTEIN A147T, 90% H2O/10% D2O90% H2O/10% D2O
20.3-0.7 mM [U-100% 13C; U-100% 15N] TRANSLOCATOR PROTEIN A147T, 0.3-0.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] TRANSLOCATOR PROTEIN A147T, 90% H2O/10% D2O90% H2O/10% D2O
30.3-0.7 mM [U-100% 13C; U-100% 15N] TRANSLOCATOR PROTEIN A147T, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTRANSLOCATOR PROTEIN A147T-1[U-100% 13C; U-100% 15N]0.3-0.71
mMTRANSLOCATOR PROTEIN A147T-2[U-100% 13C; U-100% 15N; U-80% 2H]0.3-0.71
mMTRANSLOCATOR PROTEIN A147T-3[U-100% 13C; U-100% 15N]0.3-0.72
mMTRANSLOCATOR PROTEIN A147T-4[U-100% 13C; U-100% 15N; U-80% 2H]0.3-0.72
mMTRANSLOCATOR PROTEIN A147T-5[U-100% 13C; U-100% 15N]0.3-0.73
Sample conditionsIonic strength: 10 / pH: 6.0 / Pressure: AMBIENT / Temperature: 315 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CYANA_3.0Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 105 / Conformers submitted total number: 20

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