5NV9

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

• PDB DOI:  https://doi.org/10.2210/pdb5NV9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Proteus mirabilis HI4320
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-05-03 Released: 2018-04-04 
• Deposition Author(s): Wahlgren, W.Y., North, R.A., Dunevall, E., Paz, A., Goyal, P., Bisignano, P., Grabe, M., Dobson, R., Abramson, J., Ramaswamy, S., Friemann, R.
• Funding Organization(s): Swedish Research Council, Swedish Governmental Agency for Innovation Systems (VINNOVA), Italian Ministry of Instruction University and Research, National Institutes of Health, Indo-Swedish grant awarded by Department of Biotechnology, Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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

• PubMed: 29717135 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Structural Biology, School of Medicine Stanford University, 299 Campus Drive West Stanford, Stanford, CA, 94305-5126, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.89 kDa 
• Atom Count: 3,998 
• Modelled Residue Count: 480 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sodium:solute symporter	A	496	Proteus mirabilis HI4320	Mutation(s): 0  Gene Names: PMI2976 Membrane Entity: Yes
UniProt
Find proteins for B4EZY7 (Proteus mirabilis (strain HI4320)) Explore B4EZY7  Go to UniProtKB:  B4EZY7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	E [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
SLB	D [auth A]	N-acetyl-beta-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-PFQGKNLYSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.59	α = 90
b = 98.07	β = 92.15
c = 54.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXS	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Wahlgren, W.Y., North, R.A., Dunevall, E., Paz, A., Goyal, P., Bisignano, P., Grabe, M., Dobson, R., Abramson, J., Ramaswamy, S., Friemann, R.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2011-5790
Swedish Research Council	Sweden	2010-1795, 221-2013-730
Swedish Governmental Agency for Innovation Systems (VINNOVA)	Sweden	2013-04655
Italian Ministry of Instruction University and Research	Italy	PON01_00937
National Institutes of Health	United States	R01GM078844, R01GM089740
Indo-Swedish grant awarded by Department of Biotechnology	India	BT/IN/Sweden/41/SR/2013
Royal Society of New Zealand	New Zealand	UOC1506

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 2.0: 2018-05-16
  Changes: Advisory, Data collection, Database references, Non-polymer description, Polymer sequence, Structure summary
• Version 2.1: 2019-10-16
  Changes: Data collection
• Version 2.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary