7ZNR | pdb_00007znr

Inactive D62N mutant of BT1760 Endo-acting levanase from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZNR

This is version 1.1 of the entry. See complete history

Literature

Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes.

White, J.B.R.Silale, A.Feasey, M.Heunis, T.Zhu, Y.Zheng, H.Gajbhiye, A.Firbank, S.Basle, A.Trost, M.Bolam, D.N.van den Berg, B.Ranson, N.A.

(2023) Nature 618: 583-589

  • DOI: https://doi.org/10.1038/s41586-023-06146-w
  • Primary Citation Related Structures: 
    7ZNR, 7ZNS, 8A9Y, 8AA0, 8AA1, 8AA2, 8AA3, 8AA4

  • PubMed Abstract: 

    Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut 1 . Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.


  • Organizational Affiliation
    • Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.

Macromolecule Content 

  • Total Structure Weight: 123.08 kDa 
  • Atom Count: 8,089 
  • Modeled Residue Count: 974 
  • Deposited Residue Count: 1,046 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sucrose-6-phosphate hydrolase
A, B
523Bacteroides thetaiotaomicronMutation(s): 1 
Gene Names: scrBBSIG_4326Btheta7330_01254
EC: 3.2.1.26
UniProt
Find proteins for Q8A6W6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6W6 
Go to UniProtKB:  Q8A6W6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6W6
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose
C, D, E
5N/A
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose
F
2N/A
Glycosylation Resources
GlyTouCan: G51829YA
GlyCosmos: G51829YA
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose
G
3N/A
Glycosylation Resources
GlyTouCan: G30220AI
GlyCosmos: G30220AI

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.72α = 90
b = 174.72β = 90
c = 215.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/F014163/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Refinement description