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- PDB-9j4r: Cryo-EM structure of ferric ion importer, FbpBC, from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 9j4r
TitleCryo-EM structure of ferric ion importer, FbpBC, from Thermus thermophilus
Components
  • Iron ABC transporter permease
  • Iron ABC transporter, ATP-binding protein
KeywordsMEMBRANE PROTEIN / Fe3+ ion transporter / ABC importer / ABC transporter
Function / homology
Function and homology information


ABC-type ferric iron transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, ferric cation import, FbpC / : / Transport-associated OB, type 2 / TOBE domain / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site ...ABC transporter, ferric cation import, FbpC / : / Transport-associated OB, type 2 / TOBE domain / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Iron ABC transporter permease / Iron ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLu, P. / Nagata, K. / Kise, Y. / Nureki, O.
Funding support Japan, China, 14items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K22561 Japan
Other privateJapan Science Society 2023-4016 Japan
Other privateInnovation Center of Yangtze River Delta, Zhejiang University, Research Start-up Project China
Japan Society for the Promotion of Science (JSPS)19H05771 Japan
Japan Society for the Promotion of Science (JSPS)17681026 Japan
Japan Society for the Promotion of Science (JSPS)18H02151 Japan
Japan Society for the Promotion of Science (JSPS)22K19263 Japan
Japan Society for the Promotion of Science (JSPS)22H02555 Japan
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
Japan Science and Technology20344981 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101001 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121002 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Other privateThe Toyo Suisan Foundation, Scientific Research Grant 2024 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of ferric ion importer, FbpBC, from Thermus thermophilus HB8
Authors: Lu, P. / Nagata, K. / Kise, Y. / Nureki, O.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron ABC transporter permease
B: Iron ABC transporter, ATP-binding protein
C: Iron ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)126,8413
Polymers126,8413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Iron ABC transporter permease


Mass: 53043.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHB5018_17360 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7R7TPN0
#2: Protein Iron ABC transporter, ATP-binding protein


Mass: 36898.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA1630 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHV0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TtFbpBC / Type: COMPLEX
Details: Ferric ion binding protein BC complex from Thermus thermophilus
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1375345 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039127
ELECTRON MICROSCOPYf_angle_d0.55312409
ELECTRON MICROSCOPYf_dihedral_angle_d3.8381299
ELECTRON MICROSCOPYf_chiral_restr0.0391440
ELECTRON MICROSCOPYf_plane_restr0.0061604

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