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- EMDB-49565: E. coli Cir in Complex with the RBD of Microcin V -

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Basic information

Entry
Database: EMDB / ID: EMD-49565
TitleE. coli Cir in Complex with the RBD of Microcin V
Map data
Sample
  • Complex: E. coli Cir in Complex with the RBD of Microcin V
    • Protein or peptide: Colicin I receptor
    • Protein or peptide: Colicin-V
KeywordsTonB-dependent receptor / beta barrel / antimicrobial protein / MccV / MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / killing of cells of another organism / intracellular iron ion homeostasis / defense response to bacterium / extracellular region / membrane
Similarity search - Function
Microcin V bacteriocin / Microcin V bacteriocin / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like ...Microcin V bacteriocin / Microcin V bacteriocin / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
Colicin I receptor / Colicin-V
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteriaceae (enterobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMaurakis SA / Botos I / Buchanan SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into Cir-mediated killing by the antimicrobial protein Microcin V.
Authors: Stavros A Maurakis / Angela C O'Donnell / Istvan Botos / Rodolfo Ghirlando / Bryan W Davies / Susan K Buchanan /
Abstract: Drug-resistant bacteria are a global concern. Novel treatments are needed, but are difficult to develop for Gram-negative species due to the need to traverse the outer membrane to reach targets ...Drug-resistant bacteria are a global concern. Novel treatments are needed, but are difficult to develop for Gram-negative species due to the need to traverse the outer membrane to reach targets beneath. A promising solution is found in natural antibiotics which bind outer membrane receptors and co-opt them for import. Exploring this mechanism may open avenues for antibiotic development. An underappreciated class of natural antibiotics are microcins - small antimicrobial proteins secreted by certain bacteria during inter-species competition. Microcins bind outer-membrane receptors of prey species for passage into the periplasm. They have potent activity, bind specific targets, and can control pathobiont expansion and colonization. One microcin, MccV, utilizes the E. coli colicin Ia receptor, Cir, for import. Here, we report the first high-resolution structure of the Cir/MccV complex by Cryo-EM, revealing an interaction centered on an electropositive cavity within the Cir extracellular loops. We also report the affinity of MccV for Cir. Lastly, we mutagenized interacting residues and identified key contacts critical to MccV binding, import, and bacteriolysis. Future efforts may help disentangle the mechanisms of microcin killing and will assess relationships between other microcins and their targets to better understand the potential for microcins to be used as antibacterial drugs.
History
DepositionMar 5, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49565.png

Downloads & links

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Map

FileDownload / File: emd_49565.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.2033532 - 0.4795409
Average (Standard dev.)-0.00090758206 (±0.014677139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49565_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49565_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli Cir in Complex with the RBD of Microcin V

EntireName: E. coli Cir in Complex with the RBD of Microcin V
Components
  • Complex: E. coli Cir in Complex with the RBD of Microcin V
    • Protein or peptide: Colicin I receptor
    • Protein or peptide: Colicin-V

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Supramolecule #1: E. coli Cir in Complex with the RBD of Microcin V

SupramoleculeName: E. coli Cir in Complex with the RBD of Microcin V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Colicin I receptor

MacromoleculeName: Colicin I receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 70.576594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TMVVTASSVE QNLKDAPASI SVITQEDLQR KPVQNLKDVL KEVPGVQLTN EGDNRKGVSI RGLDSSYTLI LVDGKRVNSR NAVFRHNDF DLNWIPVDSI ERIEVVRGPM SSLYGSDALG GVVNIITKKI GQKWSGTVTV DTTIQEHRDR GDTYNGQFFT S GPLIDGVL ...String:
TMVVTASSVE QNLKDAPASI SVITQEDLQR KPVQNLKDVL KEVPGVQLTN EGDNRKGVSI RGLDSSYTLI LVDGKRVNSR NAVFRHNDF DLNWIPVDSI ERIEVVRGPM SSLYGSDALG GVVNIITKKI GQKWSGTVTV DTTIQEHRDR GDTYNGQFFT S GPLIDGVL GMKAYGSLAK REKDDPQNST TTDTGETPRI EGFSSRDGNV EFAWTPNQNH DFTAGYGFDR QDRDSDSLDK NR LERQNYS VSHNGRWDYG TSELKYYGEK VENKNPGNSS PITSESNTVD GKYTLPLTAI NQFLTVGGEM RHDKMSDAVN LTG GTSSKT SASQYALFVE DEWRIFEPLA LTTGVRMDDH ETYGEHWSPR AYLVYNATDT VTVKGGWATA FKAPSLLQLS PDWT SNSCR GACKIVGSPD LKPETSESWE LGLYYMGEEG WLEGVESSVT VFRNDVKDRI SISRTSDVNA APGYQNFVGF ETGAN GRRI PVFSYYNVNK ARIQGVETEL KIPFNDEWKL SINYTYNDGR DVSNGENKPL SDLPFHTANG TLDWKPLALE DWSMYM SGH YTGQKRADSA TAKTPGGYTI WNTGAAWQVT KDVKLRAGVL NLGDKDLSRD DYSYNEDGRR YFMAVDYRF

UniProtKB: Colicin I receptor

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Macromolecule #2: Colicin-V

MacromoleculeName: Colicin-V / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteriaceae (enterobacteria)
Molecular weightTheoretical: 3.564979 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KQKPEGIPSE AWNYAAGRLC NWSPNNLSDV CL

UniProtKB: Colicin-V

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: Phosphate Buffered Saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force +5 Wait time 0 Blot total 1 Blot time 5 seconds.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2 multimer prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 102419
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9nn6:
E. coli Cir in Complex with the RBD of Microcin V

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