4CU4

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

PDB DOI: https://doi.org/10.2210/pdb4CU4/pdb

Classification: TRANSPORT PROTEIN/ANTIBIOTIC
Organism(s): Escherichia coli str. K-12 substr. MG1655, Escherichia coli str. K-12 substr. MC4100
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2014-03-17 Released: 2014-04-09
Deposition Author(s): Mathavan, I., Rebuffat, S., Beis, K.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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

PubMed: 24705590 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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. 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.

Macromolecule Content

Total Structure Weight: 88.63 kDa
Atom Count: 6,260
Modelled Residue Count: 714
Deposited Residue Count: 727
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERRICHROME-IRON RECEPTOR	A	706	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06971 (Escherichia coli (strain K12)) Explore P06971 Go to UniProtKB: P06971
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06971
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MICROCIN J25	B	21	Escherichia coli str. K-12 substr. MC4100	Mutation(s): 0
UniProt
Find proteins for Q9X2V7 (Escherichia coli) Explore Q9X2V7 Go to UniProtKB: Q9X2V7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X2V7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	C	6		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G23424DU GlyCosmos: G23424DU

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PH Query on 3PH Download Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain BA [auth A]	BA [auth A]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
FTT Query on FTT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], H [auth A]	3-HYDROXY-TETRADECANOIC ACID C₁₄ H₂₈ O₃ ATRNZOYKSNPPBF-CYBMUJFWSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain AA [auth A] SDF format, chain O [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	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		Interactions Focus chain AA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
DPO Query on DPO Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain GA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain GA [auth A]	EA [auth A], GA [auth A]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain EA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain HA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain HA [auth A]	FA [auth A], HA [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FA [auth A] Focus chain HA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain HA [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000184 Query on PRD_000184	B	Microcin J25	Polypeptide / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

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 = 95.98	α = 90
b = 277.05	β = 90
c = 106.76	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-09

Deposition Author(s):

Mathavan, I.

Rebuffat, S.

Beis, K.

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
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary