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- PDB-8hmf: head module state 2 of Tetrahymena IFT-A -

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Basic information

Entry
Database: PDB / ID: 8hmf
Titlehead module state 2 of Tetrahymena IFT-A
Components
  • Intraflagellar transport protein 122 homolog
  • Intraflagellar transporter
  • WD40 repeat protein
KeywordsPROTEIN TRANSPORT / intraflagellar transport complex
Function / homology
Function and homology information


intraciliary transport particle A / cellular component assembly / intraciliary retrograde transport / protein localization to cilium / non-motile cilium assembly / non-motile cilium / axoneme / cilium assembly / cilium / ciliary basal body
Similarity search - Function
WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / : / : / : / WDR19 second beta-propeller / IFT140 first beta-propeller / IFT140 second beta-propeller / WDR19 first beta-propeller / IF140 C-terminal TPR domain ...WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / : / : / : / WDR19 second beta-propeller / IFT140 first beta-propeller / IFT140 second beta-propeller / WDR19 first beta-propeller / IF140 C-terminal TPR domain / : / IF140/IFT172 TPR domain / Intraflagellar transport protein 122 homolog / : / : / IFT122 second beta-propeller / IFT122 first beta-propeller / IFT122, TPR domain / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Intraflagellar transporter / WD40 repeat protein / Intraflagellar transport protein 122 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsMa, Y. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionDec 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_database_status
Item: _em_admin.last_update / _pdbx_database_status.pdb_format_compatible

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intraflagellar transport protein 122 homolog
D: Intraflagellar transporter
E: WD40 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,1275
Polymers463,9963
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Intraflagellar transport protein 122 homolog


Mass: 143939.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q244W3
#2: Protein Intraflagellar transporter / intraflagellar transport 140


Mass: 161644.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LVZ7
#3: Protein WD40 repeat protein / intraflagellar transport 144


Mass: 158411.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22BP2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: IFT-A_head-2 / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.4
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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199946 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00225803
ELECTRON MICROSCOPYf_angle_d0.55834820
ELECTRON MICROSCOPYf_dihedral_angle_d4.5263389
ELECTRON MICROSCOPYf_chiral_restr0.0423819
ELECTRON MICROSCOPYf_plane_restr0.0034499

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