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- EMDB-61136: Cryo-EM structure of ferric ion importer, FbpBC, from Thermus the... -

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Basic information

Entry
Database: EMDB / ID: EMD-61136
TitleCryo-EM structure of ferric ion importer, FbpBC, from Thermus thermophilus
Map datamain map
Sample
  • Complex: TtFbpBC
    • Protein or peptide: Iron ABC transporter permease
    • Protein or peptide: Iron ABC transporter, ATP-binding protein
KeywordsFe3+ ion transporter / ABC importer / ABC transporter / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLu P / Nagata K / Kise Y / Nureki O
Funding support Japan, China, 14 items
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, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61136.png

Downloads & links

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Map

FileDownload / File: emd_61136.map.gz / Format: CCP4 / Size: 101 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 Å/pix.
x 298 pix.
= 298.8 Å		1 Å/pix.
x 298 pix.
= 298.8 Å		1 Å/pix.
x 298 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.456123 - 6.811709
Average (Standard dev.)-0.0020122128 (±0.11051709)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions298298298
Spacing298298298
CellA=B=C: 298.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61136_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_61136_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_61136_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 : TtFbpBC

EntireName: TtFbpBC
Components
  • Complex: TtFbpBC
    • Protein or peptide: Iron ABC transporter permease
    • Protein or peptide: Iron ABC transporter, ATP-binding protein

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Supramolecule #1: TtFbpBC

SupramoleculeName: TtFbpBC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Ferric ion binding protein BC complex from Thermus thermophilus
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #1: Iron ABC transporter permease

MacromoleculeName: Iron ABC transporter permease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 53.043777 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AGVLLPVAYL GVRALEADPL VLREILLRPK NLELLRNTLG LAAGVLGLAT LVALPAAYLT TRTDLRGKRL WATLLTLPLA VPGYVGAYV LLSATGPGGL LPLPRPEGYW GALLVLGLIT YPYLFLALRA AFLGVDPSVE EAARTLGHPP WRVFLRVTLP Q LLPAFLSG ...String:
AGVLLPVAYL GVRALEADPL VLREILLRPK NLELLRNTLG LAAGVLGLAT LVALPAAYLT TRTDLRGKRL WATLLTLPLA VPGYVGAYV LLSATGPGGL LPLPRPEGYW GALLVLGLIT YPYLFLALRA AFLGVDPSVE EAARTLGHPP WRVFLRVTLP Q LLPAFLSG YLVIALHVLG DFGTVSLLRY ETFSYAIYLQ YSAAFDRVYA AWLALFLLLL TGSLLLLEAA LLRRLSLGRT GR GAARTSP PARLGPLAPL AHLFLLLPFL LAVAFPLYAL LHLARRFPAS ATSGLAEALG HALLVALPVA FLSVGMALPI AYL ASRYPS AASRTLERLA YLAYAIPPLA YALAWIFFSL RTLPFLYGTL ALLVLALALH FLTESLGPVR SALAQVPPRL EEAA RTLGD TPTRAFFRVT FPLLWRGAAA GGSLAFIGAM KELPITLLLA PTGFSTLATR VFGYTQEAMF AEAAPFALLI VGLSA AFVG VLLWNERRF

UniProtKB: Iron ABC transporter permease

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Macromolecule #2: Iron ABC transporter, ATP-binding protein

MacromoleculeName: Iron ABC transporter, ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 36.898641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MERAPLLELK GIRKRFGELE VLRGVDLALY PGEILALLGP SGCGKTTLLR VVAGLEVPDA GRVFLEGRDI TALPPEKRGI GFVFQDYAL FPHLTALGNV AFGLKGKDRL ARARKALERV GMTLFQDRRP GELSGGQQQR VALARALAPG PKLVLLDEPF S SLDAGLRA ...String:
MERAPLLELK GIRKRFGELE VLRGVDLALY PGEILALLGP SGCGKTTLLR VVAGLEVPDA GRVFLEGRDI TALPPEKRGI GFVFQDYAL FPHLTALGNV AFGLKGKDRL ARARKALERV GMTLFQDRRP GELSGGQQQR VALARALAPG PKLVLLDEPF S SLDAGLRA ATREEVRKVL KETGTAALLV THDQEEALSF ADRLGVMRGG EILQVGTPEE VYLRPKTPFV AQFLGRTNLL PG EGRGRYA ETCLGRVPLA EAREGPLLLS LRPEALRLTP PGQGPQGEVV AREFKGHDLT YRVRLHGVQP EREVLVQEGP TCP FKVGDR VGLEVVGEGV ALEG

UniProtKB: Iron ABC transporter, ATP-binding protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: OTHER / Details: Alphafold2 prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1375345
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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