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- EMDB-35640: Cryo-EM structure of heme transporter CydDC from Mycobacterium sm... -

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Basic information

Entry
Database: EMDB / ID: EMD-35640
TitleCryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the inward facing apo state
Map data
Sample
  • Complex: CydDC
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter cydD
    • Protein or peptide: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
KeywordsABC transporter / Heme / TRANSPORT PROTEIN
Function / homology
Function and homology information


sulfate-transporting ATPase / cysteine transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
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 ...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
Transmembrane ATP-binding protein ABC transporter cydD / Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhu C / Li J
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300900 China
Ministry of Science and Technology (MoST, China)2022YFC2302900 China
Other government22ZR1441600
Other governmentZD2021CY1001
Other governmentLG202101-01-08
CitationJournal: Protein Cell / Year: 2023
Title: Cryo-EM structures of a prokaryotic heme transporter CydDC.
Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / ...Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / Haitao Yang / Zihe Rao / Jun Li /
History
DepositionMar 14, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35640.png

Downloads & links

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Map

FileDownload / File: emd_35640.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-1.0945066 - 2.1225433
Average (Standard dev.)0.0020883128 (±0.059896324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35640_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35640_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CydDC

EntireName: CydDC
Components
  • Complex: CydDC
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter cydD
    • Protein or peptide: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC

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Supramolecule #1: CydDC

SupramoleculeName: CydDC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Transmembrane ATP-binding protein ABC transporter cydD

MacromoleculeName: Transmembrane ATP-binding protein ABC transporter cydD
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: sulfate-transporting ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 53.259984 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: SYFQSNVVIA GCTIASAVVL AHIVAGIITN PATALGGETD WAPGLVALAV LWSVRVVAQW FQGRLSQRGA TAVIGELSRQ VLSSVTTSS PRRLAADRDS AAAVVTRGLD GLRPYFTGYL PAVVLAGILT PAALVVMAAY DWQAAAIVVI ALPLIPIFMV L IGLLTAER ...String:
SYFQSNVVIA GCTIASAVVL AHIVAGIITN PATALGGETD WAPGLVALAV LWSVRVVAQW FQGRLSQRGA TAVIGELSRQ VLSSVTTSS PRRLAADRDS AAAVVTRGLD GLRPYFTGYL PAVVLAGILT PAALVVMAAY DWQAAAIVVI ALPLIPIFMV L IGLLTAER SAAALTAMTT LQGRMLDLIA GIPTLRAVGR AGGSVQRIAE LSASHRRSTM ATLRISFLSA LVLELLATLG VA LVAVSVG LRLVFGDMTL AAGLTALLLA PEVFWPLRRV GAAFHAAQDG KTAAEQALRL CAEPHPPTGH EVVPAGAPVI EVP ALKAVM EPGRVTVLTG PNGVGKSTLL QAILGLQESP CGPILVAGVE VGALDRSAWW GRLAWMPHRP VLVPGTVREN LELL GPVPG LDEVCRSVGF DEVLGELPDG SETPLGRGGV GLSLGQRQRL GLVRALGAPA DVLLLDEPTA HLDGALEDRV LAAIV ARAR AGATVVMVGH RAPVLAAADH VVTMESSLVA P

UniProtKB: Transmembrane ATP-binding protein ABC transporter cydD

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Macromolecule #2: Component linked with the assembly of cytochrome' ABC transporter...

MacromoleculeName: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 54.821535 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: VPLLRHDPLL RLTLELLRPR LGRFLLAAAL GVLSLGSALA LAGISAWLIT RAWQMPPVLD LTVAVVAVRA LGISRGVLGY CQRLASHDS ALRAAANART GLYRKLADAP PDEAMRLPSG ELVARLGPAV DELADVLVRA LLPIVVAVVL GCAAVGVIAV I SPASAAVL ...String:
VPLLRHDPLL RLTLELLRPR LGRFLLAAAL GVLSLGSALA LAGISAWLIT RAWQMPPVLD LTVAVVAVRA LGISRGVLGY CQRLASHDS ALRAAANART GLYRKLADAP PDEAMRLPSG ELVARLGPAV DELADVLVRA LLPIVVAVVL GCAAVGVIAV I SPASAAVL AVCLVVAGVV APALAARAAH ASETVAAEHR SQRDTAGMLA LEHAPELRVS GRLDSVIATF ERHHRAWGEA AD RAAAPAA VAAAMPTAAM GVSVVGAVIA GIALAPTVAP TTAAILMLLP LSAFEATTAL PDAAAQLMRS RVAARRLLEL TTP TPLRSR PDVATVDLAP GDRLAVVGPS GSGKTTMLMA IADRLNGAGG ETPQRAAVFA EDAHLFDTTV RDNLLVVRGD ATDT ELVAA LDRVGLGEWL AGLPDGLSTV LVGGAAAVSA GQRRRLLIAR ALISAFPVVL LDEPTENLDA GDARQMLEGL LTPGA LFAA DRTVVVATHH LPPGFDCPIV RCTGRLAVAG RYLGGIKAFD YKDDDDK

UniProtKB: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107090

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