7U8P image
Entry Detail
PDB ID:
7U8P
EMDB ID:
Title:
Structure of porcine kidney V-ATPase with SidK, Rotary State 1
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2022-03-09
Release Date:
2022-07-06
Method Details:
Experimental Method:
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:V-type proton ATPase catalytic subunit A
Chain IDs:A, B, C
Chain Length:617
Number of Molecules:3
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Vacuolar proton pump subunit B
Chain IDs:D, E, F
Chain Length:351
Number of Molecules:3
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit C
Chain IDs:G
Chain Length:155
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit D
Chain IDs:H
Chain Length:247
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit E 1
Chain IDs:I, J, K
Chain Length:226
Number of Molecules:3
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit F
Chain IDs:L
Chain Length:119
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit G
Chain IDs:M, N, O
Chain Length:118
Number of Molecules:3
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Bacterial effector protein SidK
Chain IDs:P (auth: Q), Q (auth: R), R (auth: S)
Chain Length:337
Number of Molecules:3
Biological Source:Legionella pneumophila
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit H
Chain IDs:S (auth: T)
Chain Length:483
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit a
Chain IDs:T (auth: a)
Chain Length:617
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase 21 kDa proteolipid subunit isoform 1
Chain IDs:U (auth: b)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:ATPase H+ transporting accessory protein 1
Chain IDs:V (auth: c)
Chain Length:469
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit
Chain IDs:W (auth: d)
Chain Length:351
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit
Chain IDs:X (auth: e)
Chain Length:515
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Ribonuclease kappa
Chain IDs:Y (auth: f)
Chain Length:515
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:V-type proton ATPase proteolipid subunit
Chain IDs:Z (auth: g), AA (auth: h), BA (auth: i), CA (auth: j), DA (auth: k), EA (auth: l), FA (auth: m), GA (auth: n), HA (auth: o)
Chain Length:155
Number of Molecules:9
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:ATPase H(+)-transporting lysosomal accessory protein 2
Chain IDs:IA (auth: p)
Chain Length:351
Number of Molecules:1
Biological Source:Sus scrofa
Ligand Molecules
Primary Citation
CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7.
Life Sci Alliance 5 ? ? (2022)
PMID: 35794005 DOI: 10.26508/lsa.202201527

Abstact

V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7's TLDc domain interacts with V-ATPase's stator, whereas its C-terminal α helix binds V-ATPase's rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme's activity.

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Primary Citation of related structures