8HMD | pdb_00008hmd

Deposited: 2022-12-03 Released: 2023-06-14
Deposition Author(s): Ma, Y., Wu, J., Lei, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

(2023) Nat Commun 14: 1506-1506

PubMed 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 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.

Organizational Affiliation

Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intraflagellar transport protein 122 homolog	A	1,251	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q244W3 (Tetrahymena thermophila (strain SB210)) Explore Q244W3 Go to UniProtKB: Q244W3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q244W3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WD40 repeat protein	B	1,195	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q22U89 (Tetrahymena thermophila (strain SB210)) Explore Q22U89 Go to UniProtKB: Q22U89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q22U89
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetratricopeptide repeat protein	C	1,334	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for I7MFN3 (Tetrahymena thermophila (strain SB210)) Explore I7MFN3 Go to UniProtKB: I7MFN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7MFN3
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Intraflagellar transport protein 43 homolog	D [auth F]	146	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q22NF5 (Tetrahymena thermophila (strain SB210)) Explore Q22NF5 Go to UniProtKB: Q22NF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q22NF5
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]