5GXB | pdb_00005gxb

crystal structure of a LacY/Nanobody complex

• PDB DOI: https://doi.org/10.2210/pdb5GXB/pdb

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


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.346 (Depositor), 0.352 (DCC) 
• R-Value Work: 
  0.340 (Depositor), 0.345 (DCC) 
• R-Value Observed: 
  0.340 (Depositor) 

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

• PubMed: 27791182 
• DOI: https://doi.org/10.1073/pnas.1615414113
• Primary Citation 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 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.

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Organizational Affiliation: 
• State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
Department of Physiology, University of California, Los Angeles, CA 90095.
Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan.
Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
VIB Center for Structural Biology Research, VIB, 1050 Brussels, Belgium.
Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
Department of Physiology, University of California, Los Angeles, CA 90095; [e-mail].
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095.
Molecular Biology Institute, University of California, Los Angeles, CA 90095.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.31 kDa 
• Atom Count: 4,121 
• Modeled Residue Count: 519 
• Deposited Residue Count: 563 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose permease	A	423	Escherichia coli K-12	Mutation(s): 0  Gene Names: lacY, b0343, JW0334 Membrane Entity: Yes
UniProt
Find proteins for P02920 (Escherichia coli (strain K12)) Explore P02920  Go to UniProtKB:  P02920

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	B	140	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.346 (Depositor), 0.352 (DCC) 
• R-Value Work:  0.340 (Depositor), 0.345 (DCC) 
• R-Value Observed: 0.340 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.543	α = 90
b = 96.543	β = 90
c = 145.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Jiang, X., Wu, J.P., Yan, N., Kaback, H.R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1547801
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01 GM120043
Ministry of Science and Technology (MoST, China)	China	2011CB910501
National Natural Science Foundation of China (NSFC)	China	31125009 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
• Version 1.5: 2022-10-12
  Changes: Database references, Other
• Version 1.6: 2024-05-22
  Changes: Data collection