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Structure paper

TitleStructures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Journal, issue, pagesMol Cell, Vol. 80, Issue 3, Page 501-511.e3, Year 2020
Publish dateNov 5, 2020
AuthorsLongfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu /
PubMed AbstractVesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.
External linksMol Cell / PubMed:33065002 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.6 Å
Structure data

21844

6wlw

EMDB-21844, PDB-6wlw:
The Vo region of human V-ATPase in state 1 (focused refinement)
Method: EM (single particle) / Resolution: 3.0 Å

21845

6wlz

EMDB-21845, PDB-6wlz:
The V1 region of human V-ATPase in state 1 (focused refinement)
Method: EM (single particle) / Resolution: 2.9 Å

21847

6wm2

EMDB-21847, PDB-6wm2:
Human V-ATPase in state 1 with SidK and ADP
Method: EM (single particle) / Resolution: 3.1 Å

21848

6wm3

EMDB-21848, PDB-6wm3:
Human V-ATPase in state 2 with SidK and ADP
Method: EM (single particle) / Resolution: 3.4 Å

21849

6wm4

EMDB-21849, PDB-6wm4:
Human V-ATPase in state 3 with SidK and ADP
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-WSS:
tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

ChemComp-WJS:
(2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid

ChemComp-CLR:
CHOLESTEROL

ChemComp-PSF:
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

ChemComp-WJP:
methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
  • Legionella pneumophila subsp. pneumophila (bacteria)
  • legionella pneumophila subsp. pneumophila (strain philadelphia 1 / atcc 33152 / dsm 7513) (bacteria)
  • legionella pneumophila (bacteria)
KeywordsMEMBRANE PROTEIN / V-ATPase / proton pump / pump

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