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- PDB-8ipr: Cryo-EM structure of heme transporter CydDC from Mycobacterium sm... -

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Basic information

Entry
Database: PDB / ID: 8ipr
TitleCryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the outward facing ATP bound state
Components
  • Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
  • Transmembrane ATP-binding protein ABC transporter cydD
KeywordsTRANSPORT PROTEIN / ABC transporter / Heme
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 / ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / 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, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhu, C. / Li, J.
Funding support China, 5items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
C: Transmembrane ATP-binding protein ABC transporter cydD
D: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
E: Transmembrane ATP-binding protein ABC transporter cydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,40412
Polymers210,2784
Non-polymers2,1268
Water00
1
A: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
C: Transmembrane ATP-binding protein ABC transporter cydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2026
Polymers105,1392
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
D: Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC
E: Transmembrane ATP-binding protein ABC transporter cydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2026
Polymers105,1392
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 51880.230 Da / Num. of mol.: 2 / Mutation: E458Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: cydC / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A8B4R833
#2: Protein Transmembrane ATP-binding protein ABC transporter cydD


Mass: 53259.000 Da / Num. of mol.: 2 / Mutation: E456Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: cydD, NCTC7017_05649 / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: A0A8B4R4Z5, sulfate-transporting ATPase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: CydDC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158908 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315152
ELECTRON MICROSCOPYf_angle_d0.65420770
ELECTRON MICROSCOPYf_dihedral_angle_d4.8862214
ELECTRON MICROSCOPYf_chiral_restr0.0392592
ELECTRON MICROSCOPYf_plane_restr0.0062656

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