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Yorodumi- PDB-8j5t: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the ca... -
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-Basic information
Entry | Database: PDB / ID: 8j5t | |||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / OppABCD / ATP-Mg / Occluded state / Type I ABC importer | |||||||||
Function / homology | Function and homology information Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / peptide transport / protein import / peptide transmembrane transporter activity / 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 / peptide transport / protein import / peptide transmembrane transporter activity / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / peptide binding / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Yang, X. / Hu, T. / Zhang, B. / Rao, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j5t.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j5t.ent.gz | 240.6 KB | Display | PDB format |
PDBx/mmJSON format | 8j5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j5t_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8j5t_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8j5t_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 8j5t_validation.cif.gz | 94.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/8j5t ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j5t | HTTPS FTP |
-Related structure data
Related structure data | 35993MC 8j5qC 8j5rC 8j5sC 8j5uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Uncharacterized ... , 2 types, 2 molecules AD
#1: Protein | Mass: 64501.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv1280c, MTCY50.02 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WGU5 |
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#4: Protein | Mass: 65342.793 Da / Num. of mol.: 1 / Mutation: E180D,E525D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv1281c, MTCY50.01 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WQJ5 |
-Putative peptide transport permease protein ... , 2 types, 2 molecules BC
#2: Protein | Mass: 35120.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv1283c, MTCY373.02c Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WFZ7 |
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#3: Protein | Mass: 31402.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv1282c, MTCY373.01c, MTCY3H3.01 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WFZ9 |
-Non-polymers , 3 types, 5 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SF4 / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60489 / Symmetry type: POINT | ||||||||||||||||||||||||
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