4UC1 | pdb_00004uc1

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

PDB DOI: https://doi.org/10.2210/pdb4UC1/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Cereibacter sphaeroides
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2014-08-13 Released: 2015-02-04
Deposition Author(s): Li, F., Liu, J., Zheng, Y., Garavito, R.M., Ferguson-Miller, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan State University Strategic Partnership Grant, Mitochondrial Science & Medicine

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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

PubMed: 25635101 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1260590
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 61.45 kDa
Atom Count: 4,330
Modeled Residue Count: 462
Deposited Residue Count: 471
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocator protein TspO	A, B, C	157	Cereibacter sphaeroides	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for Q9RFC8 (Cereibacter sphaeroides) Explore Q9RFC8 Go to UniProtKB: Q9RFC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RFC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Z0P Query on Z0P Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	(2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate C₃₇ H₇₀ O₅ IIEPDWHEGOSXLD-NMYQGLQJSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
PP9 Query on PP9 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	PROTOPORPHYRIN IX C₃₄ H₃₄ N₄ O₄ FEDYMSUPMFCVOD-UJJXFSCMSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
P4C Query on P4C Download:Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C₁₄ H₂₈ O₈ CTLLATPOKUEFSQ-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
MOE Query on MOE Download:Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	METHOXY-ETHOXYL C₃ H₇ O₂ ASQUQUOEFDHYGP-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.201 (Depositor), 0.203 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.632	α = 90
b = 99.544	β = 99.92
c = 95.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data scaling
XSCALE	data scaling
SHARP	phasing
PHASER	phasing
JBluIce-EPICS	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM26916
Michigan State University Strategic Partnership Grant, Mitochondrial Science & Medicine	United 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