Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

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

Macromolecule Content

• Total Structure Weight: 96541.62 
• Atom Count: 6720 
• Residue Count: 887 
• Unique protein chains: 3

3GI8

Crystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclonal Fab Fragment

• DOI: 10.2210/pdb3GI8/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• Expression System: Mus musculus, Escherichia coli
• Mutation(s): 1 


• Deposited: 2009-03-05 Released: 2009-08-18 
• Deposition Author(s): Shaffer, P.L., Goehring, A.S., Shankaranarayanan, A., Gouaux, E., New York Consortium on Membrane Protein Structure (NYCOMPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.307 
• R-Value Work: 0.254 

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

• PubMed: 19608859 
• DOI: 10.1126/science.1176088
• Primary Citation of Related Structures:  
  3GIA, 3GI9


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein MJ0609	C	444	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)	Mutation(s): 1
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Amino Acid/Polyamine/Organocation (APC) Superfamily	Protein:  apo ApcT Na+-independent Amino Acid Transporter
Find proteins for Q58026 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Go to UniProtKB:  Q58026

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
7F11 Anti-ApcT Monoclonal Fab Light Chain	L	220	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
7F11 Anti-ApcT Monoclonal Fab Heavy Chain	H	223	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.307 
• R-Value Work: 0.254 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 46.039	α = 90.00
b = 111.188	β = 90.92
c = 115.674	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-05 
• Released Date: 2009-08-18 
• Deposition Author(s): Shaffer, P.L., Goehring, A.S., Shankaranarayanan, A., Gouaux, E., New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History 

• Version 1.0: 2009-08-18
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance