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- PDB-2mgy: Solution structure of the mitochondrial translocator protein (TSP... -

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Basic information

Entry
Database: PDB / ID: 2mgy
TitleSolution structure of the mitochondrial translocator protein (TSPO) in complex with its high-affinity ligand PK11195
ComponentsTranslocator protein
KeywordsMEMBRANE PROTEIN / translocator protein (TSPO) / protein-ligand complex / mitochondrial membrane / PK11195 / DPC micelles / peripheral benzodiazepine receptor / helical membrane channel protein
Function / homology
Function and homology information


negative regulation of corticosterone secretion / Pregnenolone biosynthesis / response to vitamin B1 / negative regulation of ATP metabolic process / contact inhibition / peripheral nervous system axon regeneration / regulation of steroid biosynthetic process / maintenance of protein location in mitochondrion / establishment of protein localization to mitochondrion / glial cell migration ...negative regulation of corticosterone secretion / Pregnenolone biosynthesis / response to vitamin B1 / negative regulation of ATP metabolic process / contact inhibition / peripheral nervous system axon regeneration / regulation of steroid biosynthetic process / maintenance of protein location in mitochondrion / establishment of protein localization to mitochondrion / glial cell migration / response to acetylcholine / androgen binding / benzodiazepine receptor activity / cellular hypotonic response / negative regulation of nitric oxide biosynthetic process / steroid biosynthetic process / positive regulation of calcium ion transport / response to manganese ion / positive regulation of programmed necrotic cell death / chloride transport / negative regulation of glial cell proliferation / adrenal gland development / lipid transport / negative regulation of mitophagy / positive regulation of mitochondrial depolarization / response to testosterone / cellular response to zinc ion / behavioral response to pain / positive regulation of glial cell proliferation / negative regulation of tumor necrosis factor production / negative regulation of protein ubiquitination / response to progesterone / cholesterol homeostasis / positive regulation of reactive oxygen species metabolic process / cellular response to lipopolysaccharide / transmembrane transporter binding / mitochondrial outer membrane / positive regulation of apoptotic process / response to xenobiotic stimulus / 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
AuthorsJaremko, M. / Jaremko, L. / Giller, K. / Becker, S. / Zweckstetter, M.
CitationJournal: Science / Year: 2014
Title: Structure of the mitochondrial translocator protein in complex with a diagnostic ligand.
Authors: Jaremko, L. / Jaremko, M. / Giller, K. / Becker, S. / Zweckstetter, M.
History
DepositionNov 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 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: Translocator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1522
Polymers18,7991
Non-polymers3531
Water00
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: 18798.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tspo, Bzrp / Plasmid: pET15PBR / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D 1H-13C NOESY
11443D CBCA(CO)NH
11543D HNCO
11643D HNCA
11743D HN(CA)CB
11843D HN(CO)CA
11963D CBCA(CO)NH
12063D HNCO
12163D HNCA
12263D HN(CA)CB
12363D HN(CO)CA
12452D 1H-13C HSQC aliphatic
12553D 1H-13C NOESY aliphatic
12633D CBCA(CO)NH
12733D HNCO
12833D HNCA
12933D HN(CA)CB
13033D HN(CO)CA
13173D CBCA(CO)NH
13273D HNCO
13373D HNCA
13473D HN(CA)CB
13573D HN(CO)CA
13673D 1H-13C NOESY aliphatic
13773D 1H-13C NOESY aromatic
13822D 1H-13C HSQC aliphatic
13922D 1H-13C HSQC aromatic
14023D 1H-13C NOESY aliphatic
14123D 1H-13C NOESY aromatic
14223D (H)CCH-TOCSY
14332D 1H-15N HSQC
14442D 1H-15N HSQC
14552D 1H-15N HSQC
14662D 1H-15N HSQC
14772D 1H-15N HSQC
14822D 1H-15N HSQC
14943D 1H-15N NOESY
15062D 1H-13C HSQC aliphatic
15162D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-100% 13C; U-100% 15N] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-2H] DPC micelles, 100% D2O100% D2O
30.8 mM [U-13C; U-15N; U-2H] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-2H; U-1H, 15N,13C-TRP, ARG] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 90% H2O/10% D2O90% H2O/10% D2O
50.5 mM [U-2H,15N; Idelta1/Leu,ValproS-13CH3] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 90% H2O/10% D2O90% H2O/10% D2O
60.5 mM [U-2H; U-1H, 15N,13C-Ile,Lys,Pro,Gly] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 90% H2O/10% D2O90% H2O/10% D2O
70.5 mM [U-2H; U-1H,15N-Leu,Phe] protein, 2.9 mM PKA, 10 mM sodium phosphate buffer, 60 mM [U-100% 2H] DPC micelles, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMentity_1-1[U-100% 13C; U-100% 15N]1
2.9 mMPKA-21
10 mMsodium phosphate buffer-31
60 mMDPC micelles-4[U-100% 2H]1
0.9 mMentity_1-5[U-100% 13C; U-100% 15N]2
2.9 mMPKA-62
10 mMsodium phosphate buffer-72
60 mMDPC micelles-8[U-2H]2
0.8 mMentity_1-9[U-13C; U-15N; U-2H]3
2.9 mMPKA-103
10 mMsodium phosphate buffer-113
60 mMDPC micelles-12[U-100% 2H]3
0.5 mMentity_1-13[U-2H; U-1H, 15N,13C-TRP, ARG]4
2.9 mMPKA-144
10 mMsodium phosphate buffer-154
60 mMDPC micelles-16[U-100% 2H]4
0.5 mMentity_1-17[U-2H,15N; Idelta1/Leu,ValproS-13CH3]5
2.9 mMPKA-185
10 mMsodium phosphate buffer-195
60 mMDPC micelles-20[U-100% 2H]5
0.5 mMentity_1-21[U-2H; U-1H, 15N,13C-Ile,Lys,Pro,Gly]6
2.9 mMPKA-226
10 mMsodium phosphate buffer-236
60 mMDPC micelles-24[U-100% 2H]6
0.5 mMentity_1-25[U-2H; U-1H,15N-Leu,Phe]7
2.9 mMPKA-267
10 mMsodium phosphate buffer-277
60 mMDPC micelles-28[U-100% 2H]7
Sample conditionsIonic strength: 10 / pH: 6 / 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
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
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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