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Yorodumi- PDB-7wiw: Cryo-EM structure of Mycobacterium tuberculosis irtAB complexed w... -
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-Basic information
Entry | Database: PDB / ID: 7wiw | |||||||||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis irtAB complexed with ATP in an occluded conformation | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / IrtAB / ABC exporter-liker importer / Iron-loaded siderophore / Mycobacterium tuberculosis | |||||||||||||||
Function / homology | Function and homology information iron acquisition from host / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / Mtb iron assimilation by chelation / cellular response to iron ion starvation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / FAD binding / intracellular iron ion homeostasis ...iron acquisition from host / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / Mtb iron assimilation by chelation / cellular response to iron ion starvation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / FAD binding / intracellular iron ion homeostasis / oxidoreductase activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||||||||
Authors | Zhang, B. / Sun, S. / Yang, H. / Rao, Z. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Protein Cell / Year: 2023 Title: Cryo-EM structures for the Mycobacterium tuberculosis iron-loaded siderophore transporter IrtAB. Authors: Shan Sun / Yan Gao / Xiaolin Yang / Xiuna Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Yuting Ran / Pengxuan Ren / Fang Bai / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang / Abstract: The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import ...The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import iron-loaded siderophores. Unusually, it adopts the canonical type IV exporter fold. Herein, we report the structure of unliganded Mtb IrtAB and its structure in complex with ATP, ADP, or ATP analogue (AMP-PNP) at resolutions ranging from 2.8 to 3.5 Å. The structure of IrtAB bound ATP-Mg2+ shows a "head-to-tail" dimer of nucleotide-binding domains (NBDs), a closed amphipathic cavity within the transmembrane domains (TMDs), and a metal ion liganded to three histidine residues of IrtA in the cavity. Cryo-electron microscopy (Cryo-EM) structures and ATP hydrolysis assays show that the NBD of IrtA has a higher affinity for nucleotides and increased ATPase activity compared with IrtB. Moreover, the metal ion located in the TM region of IrtA is critical for the stabilization of the conformation of IrtAB during the transport cycle. This study provides a structural basis to explain the ATP-driven conformational changes that occur in IrtAB. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wiw.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wiw.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wiw_validation.pdf.gz | 1007.6 KB | Display | wwPDB validaton report |
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Full document | 7wiw_full_validation.pdf.gz | 1020.8 KB | Display | |
Data in XML | 7wiw_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 7wiw_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/7wiw ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wiw | HTTPS FTP |
-Related structure data
Related structure data | 32538MC 7wiuC 7wivC 7wixC 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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-Components
#1: Protein | Mass: 61008.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: irtB, Rv1349, MTCY02B10.13 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WQJ7, Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate | ||||
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#2: Protein | Mass: 93070.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: irtA, Rv1348, MTCY02B10.12 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WQJ9, Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate | ||||
#3: Chemical | #4: Chemical | 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 |
-Sample preparation
Component | Name: IrtAB / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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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 K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101408 / Symmetry type: POINT |