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- EMDB-35641: Cryo-EM structure of heme transporter CydDC from Mycobacterium sm... -

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Basic information

Entry
Database: EMDB / ID: EMD-35641
TitleCryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the outward facing ATP bound state
Map data
Sample
  • Complex: CydDC
    • Protein or peptide: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter cydD
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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: 3.0 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_35641.png

Downloads & links

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Map

FileDownload / File: emd_35641.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.31897247 - 1.2972001
Average (Standard dev.)-0.00023627297 (±0.035150018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35641_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35641_half_map_2.map
Projections & Slices
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Sample components

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Entire : CydDC

EntireName: CydDC
Components
  • Complex: CydDC
    • Protein or peptide: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter cydD
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CydDC

SupramoleculeName: CydDC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: 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: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 51.88023 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: LRHDPLLRLT LELLRPRLGR FLLAAALGVL SLGSALALAG ISAWLITRAW QMPPVLDLTV AVVAVRALGI SRGVLGYCQR LASHDSALR AAANARTGLY RKLADAPPDE AMRLPSGELV ARLGPAVDEL ADVLVRALLP IVVAVVLGCA AVGVIAVISP A SAAVLAVC ...String:
LRHDPLLRLT LELLRPRLGR FLLAAALGVL SLGSALALAG ISAWLITRAW QMPPVLDLTV AVVAVRALGI SRGVLGYCQR LASHDSALR AAANARTGLY RKLADAPPDE AMRLPSGELV ARLGPAVDEL ADVLVRALLP IVVAVVLGCA AVGVIAVISP A SAAVLAVC LVVAGVVAPA LAARAAHASE TVAAEHRSQR DTAGMLALEH APELRVSGRL DSVIATFERH HRAWGEAADR AA APAAVAA AMPTAAMGVS VVGAVIAGIA LAPTVAPTTA AILMLLPLSA FEATTALPDA AAQLMRSRVA ARRLLELTTP TPL RSRPDV ATVDLAPGDR LAVVGPSGSG KTTMLMAIAD RLNGAGGETP QRAAVFAEDA HLFDTTVRDN LLVVRGDATD TELV AALDR VGLGEWLAGL PDGLSTVLVG GAAAVSAGQR RRLLIARALI SAFPVVLLDQ PTENLDAGDA RQMLEGLLTP GALFA ADRT VVVATHHLPP GFDCPIVRCT

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

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Macromolecule #2: Transmembrane ATP-binding protein ABC transporter cydD

MacromoleculeName: Transmembrane ATP-binding protein ABC transporter cydD
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: sulfate-transporting ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 53.259 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 DVLLLDQPTA HLDGALEDRV LAAIV ARAR AGATVVMVGH RAPVLAAADH VVTMESSLVA P

UniProtKB: Transmembrane ATP-binding protein ABC transporter cydD

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158908
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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