4RYM | pdb_00004rym

Crystal structure of BcTSPO Iodo Type1 monomer

• PDB DOI: https://doi.org/10.2210/pdb4RYM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2014-12-15 Released: 2015-01-28 
• Deposition Author(s): Guo, Y., Liu, Q., Hendrickson, W.A., New York Consortium on Membrane Protein Structure (NYCOMPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.272 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Protein structure. Structure and activity of tryptophan-rich TSPO proteins.

Guo, Y., Kalathur, R.C., Liu, Q., Kloss, B., Bruni, R., Ginter, C., Kloppmann, E., Rost, B., Hendrickson, W.A.

(2015) Science 347: 551-555

• PubMed: 25635100 
• DOI: https://doi.org/10.1126/science.aaa1534
• Primary Citation Related Structures: 
  4RYI, 4RYJ, 4RYM, 4RYN, 4RYO, 4RYQ, 4RYR


• PubMed Abstract: 
  

  Translocator proteins (TSPOs) bind steroids and porphyrins, and they are implicated in many human diseases, for which they serve as biomarkers and therapeutic targets. TSPOs have tryptophan-rich sequences that are highly conserved from bacteria to mammals. Here we report crystal structures for Bacillus cereus TSPO (BcTSPO) down to 1.7 Å resolution, including a complex with the benzodiazepine-like inhibitor PK11195. We also describe BcTSPO-mediated protoporphyrin IX (PpIX) reactions, including catalytic degradation to a previously undescribed heme derivative. We used structure-inspired mutations to investigate reaction mechanisms, and we showed that TSPOs from Xenopus and man have similar PpIX-directed activities. Although TSPOs have been regarded as transporters, the catalytic activity in PpIX degradation suggests physiological importance for TSPOs in protection against oxidative stress.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
The New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
The New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA.
The New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. Department of Informatics, Bioinformatics and Computational Biology, Technische Universität München, Garching 85748, Germany.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. The New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.88 kDa 
• Atom Count: 1,259 
• Modeled Residue Count: 154 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integral membrane protein	A	181	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_3136, DSM 31 Membrane Entity: Yes
UniProt
Find proteins for Q81BL7 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81BL7  Go to UniProtKB:  Q81BL7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B [auth A], C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.272 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.356	α = 90
b = 49.538	β = 90
c = 99.213	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Guo, Y., Liu, Q., Hendrickson, W.A., New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary