4QIQ | pdb_00004qiq

Crystal structure of D-xylose-proton symporter

• PDB DOI: https://doi.org/10.2210/pdb4QIQ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2014-06-01 Released: 2014-08-06 
• Deposition Author(s): Wisedchaisri, G., Park, M., Iadanza, M.G., Zheng, H., Gonen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free: 
  0.324 (Depositor), 0.332 (DCC) 
• R-Value Work: 
  0.308 (Depositor), 0.319 (DCC) 
• R-Value Observed: 
  0.308 (Depositor) 

Starting Model: experimental

Literature

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.

Wisedchaisri, G., Park, M.S., Iadanza, M.G., Zheng, H., Gonen, T.

(2014) Nat Commun 5: 4521-4521

• PubMed: 25088546 
• DOI: https://doi.org/10.1038/ncomms5521
• Primary Citation Related Structures: 
  4QIQ


• PubMed Abstract: 
  

  The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins.

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Organizational Affiliation: 
• 1] Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA [2].
Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.25 kDa 
• Atom Count: 3,336 
• Modeled Residue Count: 439 
• Deposited Residue Count: 479 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-xylose-proton symporter	A	479	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4031, JW3991, xylE Membrane Entity: Yes
UniProt
Find proteins for P0AGF4 (Escherichia coli (strain K12)) Explore P0AGF4  Go to UniProtKB:  P0AGF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free:  0.324 (Depositor), 0.332 (DCC) 
• R-Value Work:  0.308 (Depositor), 0.319 (DCC) 
• R-Value Observed: 0.308 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.68	α = 90
b = 94.68	β = 90
c = 159.02	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Wisedchaisri, G., Park, M., Iadanza, M.G., Zheng, H., Gonen, T.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-08-27
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description