+Open data
-Basic information
Entry | Database: PDB / ID: 8hmd | ||||||
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Title | base module state 2 of Tetrahymena IFT-A | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / intraflagellar transport complex | ||||||
Function / homology | Function and homology information intraciliary transport particle A / intraciliary retrograde transport / non-motile cilium assembly / protein localization to cilium / non-motile cilium / cilium assembly / cilium Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Ma, Y. / Wu, J. / Lei, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural insight into the intraflagellar transport complex IFT-A and its assembly in the anterograde IFT train. Authors: Yuanyuan Ma / Jun He / Shaobai Li / Deqiang Yao / Chenhui Huang / Jian Wu / Ming Lei / Abstract: Intraflagellar transport (IFT) trains, the polymers composed of two multi-subunit complexes, IFT-A and IFT-B, carry out bidirectional intracellular transport in cilia, vital for cilia biogenesis and ...Intraflagellar transport (IFT) trains, the polymers composed of two multi-subunit complexes, IFT-A and IFT-B, carry out bidirectional intracellular transport in cilia, vital for cilia biogenesis and signaling. IFT-A plays crucial roles in the ciliary import of membrane proteins and the retrograde cargo trafficking. However, the molecular architecture of IFT-A and the assembly mechanism of the IFT-A into the IFT trains in vivo remains elusive. Here, we report the cryo-electron microscopic structures of the IFT-A complex from protozoa Tetrahymena thermophila. We find that IFT-A complexes present two distinct, elongated and folded states. Remarkably, comparison with the in situ cryo-electron tomography structure of the anterograde IFT train unveils a series of adjustments of the flexible arms in apo IFT-A when incorporated into the anterograde train. Our results provide an atomic-resolution model for the IFT-A complex and valuable insights into the assembly mechanism of anterograde IFT trains. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hmd.cif.gz | 610 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hmd.ent.gz | 493.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hmd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8hmd_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8hmd_validation.xml.gz | 93.4 KB | Display | |
Data in CIF | 8hmd_validation.cif.gz | 138.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hmd ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hmd | HTTPS FTP |
-Related structure data
Related structure data | 34896MC 8hmcC 8hmeC 8hmfC C: citing same article (ref.) M: map data used to model this data |
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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
#1: Protein | Mass: 143939.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q244W3 | ||
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#2: Protein | Mass: 138076.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22U89 | ||
#3: Protein | Mass: 154216.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MFN3 | ||
#4: Protein | Mass: 16711.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22NF5 | ||
#5: Chemical | Has ligand of interest | N | |
-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: IFT-A_base-2 / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Buffer solution | pH: 7.4 |
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: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86362 / Symmetry type: POINT | ||||||||||||||||||||||||
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