4CU4

FhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural Basis for Hijacking Siderophore Receptors by Antimicrobial Lasso Peptides.

Mathavan, I.Zirah, S.Mehmood, S.Choudhury, H.G.Goulard, C.Li, Y.Robinson, C.V.Rebuffat, S.Beis, K.

(2014) Nat Chem Biol 10: 340

  • DOI: 10.1038/nchembio.1499
  • Primary Citation of Related Structures:  
    4CU4

  • PubMed Abstract: 
  • The lasso peptide microcin J25 is known to hijack the siderophore receptor FhuA for initiating internalization. Here, we provide what is to our knowledge the first structural evidence on the recognition mechanism, and our biochemical data show that another closely related lasso peptide cannot interact with FhuA ...

    The lasso peptide microcin J25 is known to hijack the siderophore receptor FhuA for initiating internalization. Here, we provide what is to our knowledge the first structural evidence on the recognition mechanism, and our biochemical data show that another closely related lasso peptide cannot interact with FhuA. Our work provides an explanation on the narrow activity spectrum of lasso peptides and opens the path to the development of new antibacterials.


    Organizational Affiliation

    1] Department of Life Sciences, Imperial College London, London, UK. [2] Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire, UK. [3] Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERRICHROME-IRON RECEPTORA706Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MICROCIN J25B21Escherichia coli str. K-12 substr. MC4100Mutation(s): 0 
UniProt
Find proteins for Q9X2V7 (Escherichia coli)
Explore Q9X2V7 
Go to UniProtKB:  Q9X2V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2V7
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranoseC 6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G23424DU
GlyCosmos:  G23424DU
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
BA [auth A]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
FTT
Query on FTT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth A]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
 Ligand Interaction
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AA [auth A],
CA [auth A],
DA [auth A],
J [auth A],
K [auth A],
AA [auth A],
CA [auth A],
DA [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
I [auth A]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
DAO
Query on DAO

Download Ideal Coordinates CCD File 
G [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
DPO
Query on DPO

Download Ideal Coordinates CCD File 
EA [auth A],
GA [auth A]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
FA [auth A],
HA [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000184
Query on PRD_000184
BMicrocin J25Polypeptide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.98α = 90
b = 277.05β = 90
c = 106.76γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-04-30
    Changes: Database references
  • Version 1.3: 2018-06-13
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2020-07-01
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary