8T60

CryoEM structure of an inward-facing MelBSt at a Na(+)-bound and sugar low-affinity conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mobile barrier mechanisms for Na + -coupled symport in an MFS sugar transporter.

Hariharan, P.Shi, Y.Katsube, S.Willibal, K.Burrows, N.D.Mitchell, P.Bakhtiiari, A.Stanfield, S.Pardon, E.Kaback, H.R.Liang, R.Steyaert, J.Viner, R.Guan, L.

(2024) Elife 12

  • DOI: https://doi.org/10.7554/eLife.92462
  • Primary Citation of Related Structures:  
    8T60

  • PubMed Abstract: 

    While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na + -bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.


  • Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melibiose permease485Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: melBSTM4299
UniProt
Find proteins for P30878 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P30878 
Go to UniProtKB:  P30878
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UniProt GroupP30878
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nb725_4134synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NabFab_H ChainC [auth H]239synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NabFab_L ChainD [auth L]215synthetic constructMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONcryoSPARCcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-02-28 
  • Deposition Author(s): Guan, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM122759

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references