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- EMDB-14659: IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound st... -

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Basic information

Entry
Database: EMDB / ID: EMD-14659
TitleIF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-12)
Map dataRELION local-resolution filtered map
Sample
  • Complex: CydDC heterodimer
    • Protein or peptide: CydC
    • Protein or peptide: CydD
KeywordsABC transporter / CydDC / Heme transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type heme transporter activity / heme transmembrane transport / glutathione transmembrane transport / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type heme transporter activity / heme transmembrane transport / glutathione transmembrane transport / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell redox homeostasis / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
Glutathione/L-cysteine transport system ATP-binding/permease protein CydC / Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWu D / Safarian S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Chem Biol / Year: 2023
Title: Dissecting the conformational complexity and mechanism of a bacterial heme transporter.
Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard ...Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard Hummer / Schara Safarian /
Abstract: Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. ...Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
History
DepositionMar 29, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14659.png

Downloads & links

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Map

FileDownload / File: emd_14659.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION local-resolution filtered map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 288 pix.
= 241.056 Å		0.84 Å/pix.
x 288 pix.
= 241.056 Å		0.84 Å/pix.
x 288 pix.
= 241.056 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.12032535 - 0.19659041
Average (Standard dev.)-0.0000029413693 (±0.004238115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 241.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: RELION masked postprocessing map

Fileemd_14659_additional_1.map
AnnotationRELION masked postprocessing map
Projections & Slices
AxesZYX

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Additional map: RELION masked 3D refinement map

Fileemd_14659_additional_2.map
AnnotationRELION masked 3D refinement map
Projections & Slices
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Half map: RELION 3D refinement half map 1

Fileemd_14659_half_map_1.map
AnnotationRELION 3D refinement half map 1
Projections & Slices
AxesZYX

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Histogram

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Half map: RELION 3D refinement half map 2

Fileemd_14659_half_map_2.map
AnnotationRELION 3D refinement half map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : CydDC heterodimer

EntireName: CydDC heterodimer
Components
  • Complex: CydDC heterodimer
    • Protein or peptide: CydC
    • Protein or peptide: CydD

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Supramolecule #1: CydDC heterodimer

SupramoleculeName: CydDC heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: CydC

MacromoleculeName: CydC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGA AITRTAGRYF ERLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL L NRVVADVD TLDHLYLRVI SPLVGAFVVI MVVTIGLSFL DFTLAFTLGG ...String:
MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGA AITRTAGRYF ERLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL L NRVVADVD TLDHLYLRVI SPLVGAFVVI MVVTIGLSFL DFTLAFTLGG IMLLTLFLMP PL FYRAGKS TGQNLTHLRG QYRQQLTAWL QGQAELTIFG ASDRYRTQLE NTEIQWLEAQ RRQ SELTAL SQAIMLLIGA LAVILMLWMA SGGVGGNAQP GALIALFVFC ALAAFEALAP VTGA FQHLG QVIASAVRIS DLTDQKPEVT FPDTQTRVAD RVSLTLRDVQ FTYPEQSQQA LKGIS LQVN AGEHIAILGR TGCGKSTLLQ QLTRAWDPQQ GEILLNDSPI ASLNEAALRQ TISVVP QRV HLFSATLRDN LLLASPGSSD EALSEILRRV GLEKLLEDAG LNSWLGEGGR QLSGGEL RR LAIARALLHD APLVLLDEPT EGLDATTESQ ILELLAEMMR EKTVLMVTHR LRGLSRFQ Q IIVMDNGQII EQGTHAELLA RQGRYYQFKQ GL

UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC

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Macromolecule #2: CydD

MacromoleculeName: CydD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLL VLTFVLRAWV VWLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA G SWATLVLE QIDDMHDYYA RYLPQMALAV SVPLLIVVAI FPSNWAAALI ...String:
MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLL VLTFVLRAWV VWLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA G SWATLVLE QIDDMHDYYA RYLPQMALAV SVPLLIVVAI FPSNWAAALI LLGTAPLIPL FM ALVGMGA ADANRRNFLA LARLSGHFLD RLRGMETLRI FGRGEAEIES IRSASEDFRQ RTM EVLRLA FLSSGILEFF TSLSIALVAV YFGFSYLGEL DFGHYDTGVT LAAGFLALIL APEF FQPLR DLGTFYHAKA QAVGAADSLK TFMETPLAHP QRGEAELAST DPVTIEAEEL FITSP EGKT LAGPLNFTLP AGQRAVLVGR SGSGKSSLLN ALSGFLSYQG SLRINGIELR DLSPES WRK HLSWVGQNPQ LPAATLRDNV LLARPDASEQ ELQAALDNAW VSEFLPLLPQ GVDTPVG DQ AARLSVGQAQ RVAVARALLN PCSLLLLDEP AASLDAHSEQ RVMEALNAAS LRQTTLMV T HQLEDLADWD VIWVMQDGRI IEQGRYAELS VAGGPFATLL AHRQEEI

UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD

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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

Concentration1.5 mg/mL
BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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