ISDA

Deposition Date 2023-05-10

Release Date 2024-03-20

Last Version Date 2024-07-03

Entry Detail

PDB ID:

8P0V

Keywords:

UNKNOWN FUNCTION

Title:

Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

6.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing protein 93
Gene (Uniprot):CCDC93
Chain IDs:A (auth: K)
Chain Length:631
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q567U6 Pfam ID:PF21673, PF09762

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing protein 22
Gene (Uniprot):CCDC22
Chain IDs:B (auth: L)
Chain Length:627
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O60826 Pfam ID:PF21674, PF05667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DENN domain-containing protein 10
Gene (Uniprot):DENND10
Chain IDs:C (auth: M)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TCE6 Pfam ID:PF08616

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Vacuolar protein sorting-associated protein 29
Gene (Uniprot):VPS29
Chain IDs:D (auth: N)
Chain Length:182
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UBQ0 Pfam ID:PF12850

Protein Blast

Polymer Type:polypeptide(L)
Molecule:VPS35 endosomal protein-sorting factor-like
Gene (Uniprot):VPS35L
Chain IDs:E (auth: O)
Chain Length:963
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z3J2

Ligand Molecules

Primary Citation

Structure and interactions of the endogenous human Commander complex.

Laulumaa, S, Kumpula, E.P, Huiskonen, J.T, Varjosalo, M, Afonine, P.V, Poon, B.K, Read, R.J, Sobolev, O.V, Terwilliger, T.C, Urzhumtsev, A, Adams, P.D, Pettersen, E.F, Goddard, T.D, Huang, C.C, Meng, E.C, Couch, G.S, Croll, T.I, Morris, J.H, Ferrin, T.E.Show

Nat.Struct.Mol.Biol. 31 925 938 (2024)

PMID: 38459129 DOI: 10.1038/s41594-024-01246-1

Abstact

The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.

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Disease

Primary Citation of related structures