6FUE | pdb_00006fue

Periplasmic coiled coil domain of the FapF amyloid transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.248 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FUE

This is version 1.2 of the entry. See complete history

Literature

The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil.

Rouse, S.L.Stylianou, F.Wu, H.Y.G.Berry, J.L.Sewell, L.Morgan, R.M.L.Sauerwein, A.C.Matthews, S.

(2018) J Mol Biology 430: 3863-3871

  • DOI: https://doi.org/10.1016/j.jmb.2018.06.007
  • Primary Citation Related Structures: 
    6FUE

  • PubMed Abstract: 

    Gram-negative bacteria possess specialized biogenesis machineries that facilitate the export of amyloid subunits, the fibers of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialized outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8-Å resolution. This domain forms a novel asymmetric trimeric coiled coil that possesses a single buried tyrosine residue as well as an extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.

Macromolecule Content 

  • Total Structure Weight: 28.28 kDa 
  • Atom Count: 2,122 
  • Modeled Residue Count: 223 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FapF
A, B, C, D, E
A, B, C, D, E, F
38Pseudomonas sp. UK4Mutation(s): 0 
UniProt
Find proteins for P0DXF8 (Pseudomonas fluorescens)
Explore P0DXF8 
Go to UniProtKB:  P0DXF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DXF8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
K [auth B]
Q [auth D]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
Q [auth D],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F],
X [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
P [auth C]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
M [auth B]
N [auth B]
O [auth B]
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.248 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.59α = 90.24
b = 37.7β = 108.95
c = 57.34γ = 119.89
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Structure summary