5GXB

crystal structure of a LacY/Nanobody complex

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Escherichia coli K-12, Vicugna pacos
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-09-16 Released: 2016-10-26 
  • Deposition Author(s): Jiang, X., Wu, J.P., Yan, N., Kaback, H.R.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.340 
  • R-Value Observed: 0.340 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation.

Jiang, X.Smirnova, I.Kasho, V.Wu, J.Hirata, K.Ke, M.Pardon, E.Steyaert, J.Yan, N.Kaback, H.R.

(2016) Proc Natl Acad Sci U S A 113: 12420-12425

  • DOI: 10.1073/pnas.1615414113
  • Primary Citation of Related Structures:  
    5GXB

  • PubMed Abstract: 
  • The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane protein, catalyzes galactoside-H + symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is al ...

    The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane protein, catalyzes galactoside-H + symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar binding. We have developed single-domain camelid nanobodies (Nbs) against a mutant in an outward (periplasmic)-open conformation to stabilize this state of the protein. Here we describe an X-ray crystal structure of a complex between a double-Trp mutant (Gly46→Trp/Gly262→Trp) and an Nb in which free access to the sugar-binding site from the periplasmic cavity is observed. The structure confirms biochemical data indicating that the Nb binds stoichiometrically with nanomolar affinity to the periplasmic face of LacY primarily to the C-terminal six-helix bundle. The structure is novel because the pathway to the sugar-binding site is constricted and the central cavity containing the galactoside-binding site is empty. Although Phe27 narrows the periplasmic cavity, sugar is freely accessible to the binding site. Remarkably, the side chains directly involved in binding galactosides remain in the same position in the absence or presence of bound sugar.


    Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles, CA 90095.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lactose permeaseA423Escherichia coli K-12Mutation(s): 0 
Gene Names: lacYb0343JW0334
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
LacY Lactose Permease Transporter (G46W, G262W mutant) with bound nanobody Nb9039
Find proteins for P02920 (Escherichia coli (strain K12))
Explore P02920 
Go to UniProtKB:  P02920
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nanobodyB140Vicugna pacosMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.340 
  • R-Value Observed: 0.340 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.543α = 90
b = 96.543β = 90
c = 145.025γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1547801
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01 GM120043
Ministry of Science and Technology (MoST, China)China2011CB910501
National Natural Science Foundation of China (NSFC)China31125009 and 91017011

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence