3GI9 | pdb_00003gi9

Crystal Structure of ApcT Transporter Bound to 7F11 Monoclonal Fab Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.296 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3GI9

This is version 1.3 of the entry. See complete history

Literature

Structure and mechanism of a na+-independent amino Acid transporter.

Shaffer, P.L.Goehring, A.Shankaranarayanan, A.Gouaux, E.

(2009) Science 325: 1010-1014

  • DOI: https://doi.org/10.1126/science.1176088
  • Primary Citation Related Structures: 
    3GI8, 3GI9, 3GIA

  • PubMed Abstract: 

    Amino acid, polyamine, and organocation (APC) transporters are secondary transporters that play essential roles in nutrient uptake, neurotransmitter recycling, ionic homeostasis, and regulation of cell volume. Here, we present the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 angstrom resolution. The structure contains 12 transmembrane helices, with the first 10 consisting of an inverted structural repeat of 5 transmembrane helices like the leucine transporter LeuT. The ApcT structure reveals an inward-facing, apo state and an amine moiety of lysine-158 located in a position equivalent to the sodium ion site Na2 of LeuT. We propose that lysine-158 is central to proton-coupled transport and that the amine group serves the same functional role as the Na2 ion in LeuT, thus demonstrating common principles among proton- and sodium-coupled transporters.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.

Macromolecule Content 

  • Total Structure Weight: 96.6 kDa 
  • Atom Count: 6,865 
  • Modeled Residue Count: 873 
  • Deposited Residue Count: 887 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7F11 Anti-ApcT Monoclonal Fab Light ChainA [auth L]220Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
7F11 Anti-ApcT Monoclonal Fab Heavy ChainB [auth H]223Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein MJ0609444Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0609
Membrane Entity: Yes 
UniProt
Find proteins for Q58026 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58026 
Go to UniProtKB:  Q58026
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58026
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.296 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.365α = 90
b = 45.9β = 97.75
c = 158.088γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-07
    Changes: Database references, Other
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary