8E7F | pdb_00008e7f

Crystal structure of the autotransporter Ssp from Serratia marcescens.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.202 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8E7F

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a subtilisin-like autotransporter passenger domain reveals insights into its cytotoxic function.

Hor, L.Pilapitiya, A.McKenna, J.A.Panjikar, S.Anderson, M.A.Desvaux, M.Paxman, J.J.Heras, B.

(2023) Nat Commun 14: 1163-1163

  • DOI: https://doi.org/10.1038/s41467-023-36719-2
  • Primary Citation Related Structures: 
    8E7F

  • PubMed Abstract: 

    Autotransporters (ATs) are a large family of bacterial secreted and outer membrane proteins that encompass a wide range of enzymatic activities frequently associated with pathogenic phenotypes. We present the structural and functional characterisation of a subtilase autotransporter, Ssp, from the opportunistic pathogen Serratia marcescens. Although the structures of subtilases have been well documented, this subtilisin-like protein is associated with a 248 residue β-helix and itself includes three finger-like protrusions around its active site involved in substrate interactions. We further reveal that the activity of the subtilase AT is required for entry into epithelial cells as well as causing cellular toxicity. The Ssp structure not only provides details about the subtilase ATs, but also reveals a common framework and function to more distantly related ATs. As such these findings also represent a significant step forward toward understanding the molecular mechanisms underlying the functional divergence in the large AT superfamily.


  • Organizational Affiliation
    • Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia.

Macromolecule Content 

  • Total Structure Weight: 67.34 kDa 
  • Atom Count: 4,979 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 618 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular serine protease618Serratia marcescensMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for P09489 (Serratia marcescens)
Explore P09489 
Go to UniProtKB:  P09489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09489
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
PEG

Query on PEG



Download:Ideal Coordinates CCD File
B [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.202 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.482α = 91.52
b = 55.356β = 93.04
c = 61.883γ = 102.76
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata scaling
Auto-Rickshawphasing
BUCCANEERphasing
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP150102287
Australian Research Council (ARC)AustraliaDP180102987
Australian Research Council (ARC)AustraliaDP210100673
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1143638

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary