6IKM

Crystal structure of SpuE-Spermidine in complex with ScFv5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A Potent Anti-SpuE Antibody Allosterically Inhibits Type III Secretion System and Attenuates Virulence of Pseudomonas Aeruginosa.

Zhang, Y., Sun, X., Qian, Y., Yi, H., Song, K., Zhu, H., Zonta, F., Chen, W., Ji, Q., Miersch, S., Sidhu, S.S., Wu, D.

(2019) J Mol Biol 431: 4882-4896

  • DOI: https://doi.org/10.1016/j.jmb.2019.10.026
  • Primary Citation of Related Structures:  
    6IKM

  • PubMed Abstract: 

    • Multidrug-resistant gram-negative bacteria infection is particularly severe within the designated ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), which underscores the urgent need to explore alternative therapeutic strategies ...

    Multidrug-resistant gram-negative bacteria infection is particularly severe within the designated ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), which underscores the urgent need to explore alternative therapeutic strategies. The type III secretion system (T3SS) is considered to be a key virulence factor in many gram-negative bacteria, and T3SS is in turn regulated by SpuE in P. aeruginosa, which is a spermidine binding protein from an ATP-binding cassette transporter family and highly conserved within ESKAPE pathogens. Here, we identified a potent anti-SpuE antagonistic antibody that allosterically inhibits the expression of T3SS and attenuates virulence of P. aeruginosa. X-ray crystallography and molecular dynamics simulations revealed that binding of antibody to SpuE induces a change in the dynamics of SpuE, which in turn may reduce spermidine uptake by P. aeruginosa. The antibody could serve as a template for developing novel biologics to target a broad spectrum of gram-negative bacteria.

    Organizational Affiliation: 

    Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. Electronic address: wudh@shanghaitech.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyamine transport protein340Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for Q9I6J0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6J0 
Go to UniProtKB:  Q9I6J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I6J0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ScFv5258Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD
Download Ideal Coordinates CCD File 
AB [auth D]
BC [auth K]
DD [auth R]
FB [auth E]
FC [auth L]
AB [auth D],
BC [auth K],
DD [auth R],
FB [auth E],
FC [auth L],
JB [auth F],
JC [auth M],
MB [auth G],
NA [auth A],
PB [auth H],
QC [auth N],
SA [auth B],
TB [auth I],
WA [auth C],
XB [auth J],
XC [auth O],
YC [auth P],
ZC [auth Q]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AC [auth K]
AD [auth R]
BB [auth E]
BD [auth R]
CB [auth E]
AC [auth K],
AD [auth R],
BB [auth E],
BD [auth R],
CB [auth E],
CC [auth L],
CD [auth R],
DB [auth E],
DC [auth L],
EB [auth E],
EC [auth L],
GB [auth F],
GC [auth M],
HB [auth F],
HC [auth M],
IB [auth F],
IC [auth M],
KA [auth A],
KB [auth G],
KC [auth N],
LA [auth A],
LB [auth G],
LC [auth N],
MA [auth A],
MC [auth N],
NB [auth H],
NC [auth N],
OA [auth B],
OB [auth H],
OC [auth N],
PA [auth B],
PC [auth N],
QA [auth B],
QB [auth I],
RA [auth B],
RB [auth I],
RC [auth O],
SB [auth I],
SC [auth O],
TA [auth C],
TC [auth O],
UA [auth C],
UB [auth J],
UC [auth O],
VA [auth C],
VB [auth J],
VC [auth O],
WB [auth J],
WC [auth O],
XA [auth D],
YA [auth D],
YB [auth K],
ZA [auth D],
ZB [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.235α = 90
b = 481.804β = 120.08
c = 146.134γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2019-12-25 
    • Deposition Author(s): Wu, D., Sun, X.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31771006

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references