Structure of PDB 9b8o Chain a

Receptor sequence
>9b8oa (length=422) Species: 10116 (Rattus norvegicus) [Search protein sequence]
TYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGH
GILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGL
IYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFG
GPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIY
FKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIH
FINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQ
YLRKKHVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSE
VLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHAL
RLHWVEFQNKFYTGTGFKFLPF
3D structure
PDB9b8o High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Chaina
Resolution3.2 Å
3D
structure
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Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MAN a Q502 L503 N504 Q140 L141 N142
BS02 GLC a E493 T494 E131 T132
BS03 WJP a S535 K539 K594 S608 L609 I733 S173 K177 K232 S246 L247 I329
BS04 LP3 a L415 C467 F468 S471 L472 N473 I474 L53 C105 F106 S109 L110 N111 I112
Gene Ontology
Biological Process
GO:0007035 vacuolar acidification
GO:0008150 biological_process
GO:0016241 regulation of macroautophagy
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016471 vacuolar proton-transporting V-type ATPase complex
GO:0030665 clathrin-coated vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042470 melanosome
GO:0043195 terminal bouton
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:9b8o, PDBe:9b8o, PDBj:9b8o
PDBsum9b8o
PubMed38900912
UniProtP25286|VPP1_RAT V-type proton ATPase 116 kDa subunit a 1 (Gene Name=Atp6v0a1)

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