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- PDB-9dir: Cryo-EM structure of the heme/hemoglobin transporter ChuA, in com... -

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Basic information

Entry
Database: PDB / ID: 9dir
TitleCryo-EM structure of the heme/hemoglobin transporter ChuA, in complex with de novo designed binder G7
Components
  • ChuA binding protein G7
  • Outer membrane heme/hemoglobin receptor
KeywordsTRANSPORT PROTEIN / TonB-dependent transporter / ChuA / Heme / Hemoglobin / Outer-membrane / de novo designed protein / binding 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 speciessynthetic construct (others)
Escherichia coli CFT073 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsFox, D. / Venugopal, H. / Lupton, C.J. / Spicer, B.A. / Grinter, R.
Funding support Australia, 2items
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, D.R. / Asadollahi, K. / Samuels, I. / Spicer, B.A. / Kropp, A. / Lupton, C.J. / Lim, K. / Wang, C. / Venugopal, H. / Dramicanin, M. / Knott, G.J. / Grinter, R.
History
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ChuA binding protein G7
B: Outer membrane heme/hemoglobin receptor


Theoretical massNumber of molelcules
Total (without water)85,0202
Polymers85,0202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ChuA binding protein G7


Mass: 15433.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3
#2: Protein Outer membrane heme/hemoglobin receptor


Mass: 69586.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Gene: chuA, c4308 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: A0A0H2VC22
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between the heme/hemoglobin transporter ChuA and de novo designed binding protein G7
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: CFT073
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41 DE3
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
10.1 MolarTris1
20.15 MolarNaCl1
30.01 %Dodecyl Maltoside1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: 4D-STEM / Nominal defocus max: 1400 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131924 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046005
ELECTRON MICROSCOPYf_angle_d0.5548119
ELECTRON MICROSCOPYf_dihedral_angle_d4.116828
ELECTRON MICROSCOPYf_chiral_restr0.042873
ELECTRON MICROSCOPYf_plane_restr0.0041069

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