[English] 日本語
Yorodumi
- PDB-2mgy: Solution structure of the mitochondrial translocator protein (TSP... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of ATP metabolic process / response to vitamin B1 / contact inhibition / peripheral nervous system axon regeneration / maintenance of protein location in mitochondrion / regulation of steroid biosynthetic process / : / establishment of protein localization to mitochondrion ...negative regulation of corticosterone secretion / Pregnenolone biosynthesis / negative regulation of ATP metabolic process / response to vitamin B1 / contact inhibition / peripheral nervous system axon regeneration / maintenance of protein location in mitochondrion / regulation of steroid biosynthetic process / : / establishment of protein localization to mitochondrion / glial cell migration / benzodiazepine receptor activity / 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 / lipid transport / chloride transport / response to manganese ion / cellular response to zinc ion / negative regulation of glial cell proliferation / adrenal gland development / positive regulation of mitochondrial depolarization / cholesterol binding / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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: 6.0 / Pressure: ambient / Temperature: 315 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more