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- PDB-8j5r: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the re... -
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Basic information
Entry | Database: PDB / ID: 8j5r | |||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state | |||||||||
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![]() | MEMBRANE PROTEIN / OppABCD / Type I ABC importer / Oligopeptide permease / Mycobacterium tuberculosis | |||||||||
Function / homology | ![]() Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transmembrane transporter activity / peptide transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / peptide binding / transmembrane transport ...Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transmembrane transporter activity / peptide transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / peptide binding / transmembrane transport / protein transport / periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
![]() | Yang, X. / Hu, T. / Zhang, B. / Rao, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality. Authors: Xiaolin Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Zhenli Lin / Yao Zhao / Xiaoting Zhou / Yan Gao / Shan Sun / Xiuna Yang / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang / ![]() ![]() Abstract: Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD ...Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 297.3 KB | Display | ![]() |
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PDB format | ![]() | 236.3 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 35991MC ![]() 8j5qC ![]() 8j5sC ![]() 8j5tC ![]() 8j5uC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 64385.980 Da / Num. of mol.: 1 / Mutation: W491A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv1280c, MTCY50.02 Production host: ![]() References: UniProt: P9WGU5 |
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#2: Protein | Mass: 35120.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv1283c, MTCY373.02c Production host: ![]() References: UniProt: P9WFZ7 |
#3: Protein | Mass: 31402.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv1282c, MTCY373.01c, MTCY3H3.01 Production host: ![]() References: UniProt: P9WFZ9 |
#4: Protein | Mass: 65370.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv1281c, MTCY50.01 Production host: ![]() References: UniProt: P9WQJ5 |
#5: Chemical | ChemComp-SF4 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95101 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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