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- EMDB-46917: Cryo-EM structure of the heme/hemoglobin transporter ChuA, in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-46917
TitleCryo-EM structure of the heme/hemoglobin transporter ChuA, in complex with de novo designed binder H3
Map dataMain Map
Sample
  • Complex: Complex between the heme/hemoglobin transporter ChuA and de novo designed binding protein G7
    • Protein or peptide: ChuA Binder H3
    • Protein or peptide: Outer membrane heme/hemoglobin receptor
KeywordsTonB-dependent transporter / ChuA / Heme / Hemoglobin / Outer-membrane / de novo designed protein / binding protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


heme transmembrane transporter activity / siderophore uptake transmembrane transporter activity / cell outer membrane
Similarity search - Function
TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / 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
Outer membrane heme/hemoglobin receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others) / Escherichia coli CFT073 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsFox D / Venugopal H / Lupton CJ / Spicer BA / Grinter R
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1197376 Australia
Australian Research Council (ARC)LE200100045, LE120100090 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins
Authors: Fox DR / Asadollahi K / Samuels I / Spicer BA / Kropp A / Lupton CJ / Lim K / Wang C / Venugopal H / Dramicanin M / Knott GJ / Grinter R
History
DepositionSep 5, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46917.png

Downloads & links

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Map

FileDownload / File: emd_46917.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 260 pix.
= 262.6 Å		1.01 Å/pix.
x 260 pix.
= 262.6 Å		1.01 Å/pix.
x 260 pix.
= 262.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.748
Minimum - Maximum-4.032878 - 6.244221
Average (Standard dev.)0.0023011302 (±0.12822697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 262.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer map

Fileemd_46917_additional_1.map
AnnotationDeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_46917_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_46917_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between the heme/hemoglobin transporter ChuA and de novo ...

EntireName: Complex between the heme/hemoglobin transporter ChuA and de novo designed binding protein G7
Components
  • Complex: Complex between the heme/hemoglobin transporter ChuA and de novo designed binding protein G7
    • Protein or peptide: ChuA Binder H3
    • Protein or peptide: Outer membrane heme/hemoglobin receptor

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Supramolecule #1: Complex between the heme/hemoglobin transporter ChuA and de novo ...

SupramoleculeName: Complex between the heme/hemoglobin transporter ChuA and de novo designed binding protein G7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: CFT073

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Macromolecule #1: ChuA Binder H3

MacromoleculeName: ChuA Binder H3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.139744 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAEEAKARA AASREAAIAH VRELLKEQSD TPEMAELLRL FEAAEAADPL AAAAIAASYL AIQEYATAPP ETAATFEKYA YAAAAEAEA SPLPEAKRAA ELLRKLLDEA KAKRALEHHH HHH

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Macromolecule #2: Outer membrane heme/hemoglobin receptor

MacromoleculeName: Outer membrane heme/hemoglobin receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli CFT073 (bacteria)
Molecular weightTheoretical: 69.558164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TETMTVTATG NARSSFEAPM MVSVIDTSAP ENQTATSATD LLRHVPGITL DGTGRTNGQD VNMRGYDHRG VLVLVDGVRQ GTDTGHLNG TFLDPALIKR VEIVRGPSAL LYGSGALGGV ISYDTVDAKD LLQEGQSSGF RVFGTGGTGD HSLGLGASAF G RTENLDGI ...String:
TETMTVTATG NARSSFEAPM MVSVIDTSAP ENQTATSATD LLRHVPGITL DGTGRTNGQD VNMRGYDHRG VLVLVDGVRQ GTDTGHLNG TFLDPALIKR VEIVRGPSAL LYGSGALGGV ISYDTVDAKD LLQEGQSSGF RVFGTGGTGD HSLGLGASAF G RTENLDGI VAWSSRDRGD LRQSNGETAP NDESINNMLA KGTWQIDSAQ SLSGLVRYYN NDAREPKNPQ TVEASDSSNP MV DRSTIQR DAQLSYKLAP QGNDWLNADA KIYWSEVRIN AQNTGSSGEY REQITKGARL ENRSTLFADS FASHLLTYGG EYY RQEQHP GGATTGFPQA KIDFSSGWLQ DEITLRDLPI TLLGGTRYDS YRGSSDGYKD VDADKWSSRA GMTINPTNWL MLFG SYAQA FRAPTMGEMY NDSKHFSIGR FYTNYWVPNP NLRPETNETQ EYGFGLRFDD LMLSNDALEF KASYFDTKAK DYIST TVDF AAATTMSYNV PNAKIWGWDV MTKYTTDLFS LDVAYNRTRG KDTDTGEYIS SINPDTVTST LNIPIAHSGF SVGWVG TFA DRSTHISSSY SKQPGYGVND FYVSYQGQQA LKGMTTTLVL GNAFDKEYWS PQGIPQDGRN GKIFVSYQW

UniProtKB: Outer membrane heme/hemoglobin receptor

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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

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationName
0.1 MolarTris
0.15 MolarNaCl
0.01 %Dodecyl Maltoside
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: 4D-STEM / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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