5NVA

Substrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel Na+-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+site.

Wahlgren, W.Y.Dunevall, E.North, R.A.Paz, A.Scalise, M.Bisignano, P.Bengtsson-Palme, J.Goyal, P.Claesson, E.Caing-Carlsson, R.Andersson, R.Beis, K.Nilsson, U.J.Farewell, A.Pochini, L.Indiveri, C.Grabe, M.Dobson, R.C.J.Abramson, J.Ramaswamy, S.Friemann, R.

(2018) Nat Commun 9: 1753-1753

  • DOI: 10.1038/s41467-018-04045-7
  • Primary Citation of Related Structures:  
    5NV9, 5NVA

  • PubMed Abstract: 
  • Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids ...

    Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na + gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na + ions. One Na + binds to the conserved Na2 site, while the second Na + binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na + sites regulate N-acetylneuraminic acid transport.


    Organizational Affiliation

    Department of Structural Biology, School of Medicine Stanford University, 299 Campus Drive West Stanford, Stanford, CA, 94305-5126, USA. Rosmarie.Friemann@gu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative sodium:solute symporterA496Proteus mirabilis HI4320Mutation(s): 0 
Gene Names: PMI2976
Membrane Entity: Yes 
UniProt
Find proteins for B4EZY7 (Proteus mirabilis (strain HI4320))
Explore B4EZY7 
Go to UniProtKB:  B4EZY7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLB (Subject of Investigation/LOI)
Query on SLB

Download Ideal Coordinates CCD File 
D [auth A]N-acetyl-beta-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.788α = 90
b = 97.764β = 90
c = 151.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2011-5790
Swedish Research CouncilSweden2010-1759
Swedish Research CouncilSweden221-2013-730
The Swedish Governmental Agency for Innovation Systems (VINNOVA)Sweden2013-04655
Italian Ministry of Instruction University and ResearchItalyPON01_00937
National Institutes of HealthUnited StatesR01GM078844 and R01GM089740
Indo-Swedish grant by the Department of BiotechnologyIndiaBT/IN/Sweden/41/SR/2013
Royal Society of New ZealandNew ZealandUOC1506
Wellcome TrustUnited KingdomWT/099165/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary