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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: Maurakis SA / O'Donnell AC / Botos I / Ghirlando R / Davies BW / Buchanan SK
History
DepositionMar 5, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 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

Projections

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

Projections

Slices (1/2)
Density Histograms

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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