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- PDB-6wm4: Human V-ATPase in state 3 with SidK and ADP -

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Basic information

Entry
Database: PDB / ID: 6wm4
TitleHuman V-ATPase in state 3 with SidK and ADP
Components
  • (V-type proton ATPase ...) x 14
  • Renin receptor
  • Ribonuclease kappa
  • SidK
KeywordsMEMBRANE PROTEIN / pump
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / central nervous system maturation / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / Nef Mediated CD8 Down-regulation ...proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / central nervous system maturation / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / Nef Mediated CD8 Down-regulation / positive regulation of transforming growth factor beta1 production / ATPase-coupled ion transmembrane transporter activity / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Golgi lumen acidification / lysosomal lumen acidification / Transferrin endocytosis and recycling / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar transport / : / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / head morphogenesis / vacuolar acidification / protein localization to cilium / transmembrane transporter complex / ROS and RNS production in phagocytes / dendritic spine membrane / Nef Mediated CD4 Down-regulation / regulation of cellular pH / osteoclast development / azurophil granule membrane / ATPase activator activity / autophagosome membrane / regulation of MAPK cascade / tertiary granule membrane / microvillus / ficolin-1-rich granule membrane / proton transmembrane transporter activity / cilium assembly / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / angiotensin maturation / regulation of macroautophagy / Metabolism of Angiotensinogen to Angiotensins / enzyme regulator activity / specific granule membrane / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / RNA endonuclease activity / ruffle / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / receptor-mediated endocytosis / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / secretory granule membrane / secretory granule / cilium / transmembrane transport / synaptic vesicle membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / presynapse / apical part of cell / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / lysosome / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane
Similarity search - Function
ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like protein / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H ...ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like protein / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / Renin receptor / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A ...ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / Renin receptor / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / V-type proton ATPase subunit F / Type IV secretion protein Dot / Ribonuclease kappa / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit H / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, L. / Wu, H. / Fu, T.M.
CitationJournal: Mol Cell / Year: 2020
Title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Authors: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu /
Abstract: 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 ...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.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Assembly

Deposited unit
R: V-type proton ATPase 116 kDa subunit a isoform 1
O: V-type proton ATPase subunit C 1
J: V-type proton ATPase subunit E 1
M: V-type proton ATPase subunit G 1
I: V-type proton ATPase subunit E 1
L: V-type proton ATPase subunit G 1
H: V-type proton ATPase subunit E 1
K: V-type proton ATPase subunit G 1
S: V-type proton ATPase subunit e 1
T: Ribonuclease kappa
B: V-type proton ATPase catalytic subunit A
C: V-type proton ATPase catalytic subunit A
A: V-type proton ATPase catalytic subunit A
E: V-type proton ATPase subunit B, brain isoform
F: V-type proton ATPase subunit B, brain isoform
D: V-type proton ATPase subunit B, brain isoform
Y: SidK
Z: SidK
X: SidK
G: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
U: V-type proton ATPase subunit S1
V: Renin receptor
0: V-type proton ATPase 21 kDa proteolipid subunit
1: V-type proton ATPase 16 kDa proteolipid subunit
2: V-type proton ATPase 16 kDa proteolipid subunit
3: V-type proton ATPase 16 kDa proteolipid subunit
4: V-type proton ATPase 16 kDa proteolipid subunit
5: V-type proton ATPase 16 kDa proteolipid subunit
6: V-type proton ATPase 16 kDa proteolipid subunit
7: V-type proton ATPase 16 kDa proteolipid subunit
8: V-type proton ATPase 16 kDa proteolipid subunit
9: V-type proton ATPase 16 kDa proteolipid subunit
Q: V-type proton ATPase subunit d 1
P: V-type proton ATPase subunit H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,251,00344
Polymers1,248,80735
Non-polymers2,1979
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type proton ATPase ... , 14 types, 30 molecules ROJIHMLKSBCAEFDGNU0123456789QP

#1: Protein V-type proton ATPase 116 kDa subunit a isoform 1 / V-ATPase 116 kDa isoform a1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa isoform a1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit / Vacuolar adenosine triphosphatase subunit Ac116 / Vacuolar proton pump subunit 1 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1


Mass: 96512.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q93050
#2: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21283
#3: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / V-ATPase 31 kDa subunit / p31 / Vacuolar proton pump subunit E 1


Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36543
#4: Protein V-type proton ATPase subunit G 1 / V-ATPase subunit G 1 / V-ATPase 13 kDa subunit 1 / Vacuolar proton pump subunit G 1 / Vacuolar ...V-ATPase subunit G 1 / V-ATPase 13 kDa subunit 1 / Vacuolar proton pump subunit G 1 / Vacuolar proton pump subunit M16


Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75348
#5: Protein V-type proton ATPase subunit e 1 / V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / ...V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / Vacuolar proton pump subunit e 1


Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15342
#7: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar ATPase isoform VA68 / Vacuolar proton pump ...V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar ATPase isoform VA68 / Vacuolar proton pump subunit alpha


Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P38606, H+-transporting two-sector ATPase
#8: Protein V-type proton ATPase subunit B, brain isoform / V-ATPase subunit B 2 / Endomembrane proton pump 58 kDa subunit / HO57 / Vacuolar proton pump subunit B 2


Mass: 56561.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21281
#10: Protein V-type proton ATPase subunit D / V-ATPase subunit D / V-ATPase 28 kDa accessory protein / Vacuolar proton pump subunit D


Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5K8
#11: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16864
#12: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15904
#14: Protein V-type proton ATPase 21 kDa proteolipid subunit / V-ATPase 21 kDa proteolipid subunit / Vacuolar proton pump 21 kDa proteolipid subunit / hATPL


Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99437
#15: Protein
V-type proton ATPase 16 kDa proteolipid subunit / V-ATPase 16 kDa proteolipid subunit / Vacuolar proton pump 16 kDa proteolipid subunit


Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27449
#16: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 ...V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / p39 / Vacuolar proton pump subunit d 1


Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61421
#17: Protein V-type proton ATPase subunit H / V-ATPase subunit H / Nef-binding protein 1 / NBP1 / Protein VMA13 homolog / V-ATPase 50/57 kDa ...V-ATPase subunit H / Nef-binding protein 1 / NBP1 / Protein VMA13 homolog / V-ATPase 50/57 kDa subunits / Vacuolar proton pump subunit H / Vacuolar proton pump subunit SFD


Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI12

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Protein , 3 types, 5 molecules TYZXV

#6: Protein Ribonuclease kappa / RNase kappa


Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds
#9: Protein SidK


Mass: 65505.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A4T1L9X6, UniProt: Q5ZWW6*PLUS
#13: Protein Renin receptor / / ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal- ...ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / ER-localized type I transmembrane adaptor / Embryonic liver differentiation factor 10 / N14F / Renin/prorenin receptor / Vacuolar ATP synthase membrane sector-associated protein M8-9 / V-ATPase M8.9 subunit


Mass: 39045.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75787

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Sugars / Non-polymers , 2 types, 9 molecules

#18: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#19: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human V-ATPase with SidK and ADP / Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00673667
ELECTRON MICROSCOPYf_angle_d0.71199579
ELECTRON MICROSCOPYf_dihedral_angle_d18.28310047
ELECTRON MICROSCOPYf_chiral_restr0.04611312
ELECTRON MICROSCOPYf_plane_restr0.00412762

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