4UC1

High resolution crystal structure of translocator protein 18kDa (TSPO) from Rhodobacter sphaeroides (A139T Mutant) in C2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism.

Li, F.Liu, J.Zheng, Y.Garavito, R.M.Ferguson-Miller, S.

(2015) Science 347: 555-558

  • DOI: https://doi.org/10.1126/science.1260590
  • Primary Citation of Related Structures:  
    4UC1, 4UC2, 4UC3

  • PubMed Abstract: 

    The 18-kilodalton translocator protein (TSPO), proposed to be a key player in cholesterol transport into mitochondria, is highly expressed in steroidogenic tissues, metastatic cancer, and inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO ligands, including benzodiazepine drugs, are implicated in regulating apoptosis and are extensively used in diagnostic imaging. We report crystal structures (at 1.8, 2.4, and 2.5 angstrom resolution) of TSPO from Rhodobacter sphaeroides and a mutant that mimics the human Ala(147)→Thr(147) polymorphism associated with psychiatric disorders and reduced pregnenolone production. Crystals obtained in the lipidic cubic phase reveal the binding site of an endogenous porphyrin ligand and conformational effects of the mutation. The three crystal structures show the same tightly interacting dimer and provide insights into the controversial physiological role of TSPO and how the mutation affects cholesterol binding.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translocator protein TspO
A, B, C
157Cereibacter sphaeroidesMutation(s): 1 
UniProt
Find proteins for Q9RFC8 (Cereibacter sphaeroides)
Go to UniProtKB:  Q9RFC8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z0P
Query on Z0P

Download Ideal Coordinates CCD File 
R [auth B](2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
C37 H70 O5
IIEPDWHEGOSXLD-NMYQGLQJSA-N
PP9
Query on PP9

Download Ideal Coordinates CCD File 
J [auth A]PROTOPORPHYRIN IX
C34 H34 N4 O4
FEDYMSUPMFCVOD-UJJXFSCMSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
P4C
Query on P4C

Download Ideal Coordinates CCD File 
W [auth C]O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
MOE
Query on MOE

Download Ideal Coordinates CCD File 
X [auth C]METHOXY-ETHOXYL
C3 H7 O2
ASQUQUOEFDHYGP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.632α = 90
b = 99.544β = 99.92
c = 95.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata scaling
XSCALEdata scaling
SHARPphasing
PHASERphasing
JBluIce-EPICSdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM26916
Michigan State University Strategic Partnership Grant, Mitochondrial Science & MedicineUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references, Structure summary
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references