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- PDB-6wlz: The V1 region of human V-ATPase in state 1 (focused refinement) -

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Basic information

Entry
Database: PDB / ID: 6wlz
TitleThe V1 region of human V-ATPase in state 1 (focused refinement)
Components
  • (V-type proton ATPase subunit ...) x 5
  • SidK
  • V-type proton ATPase catalytic subunit A
KeywordsMEMBRANE PROTEIN / V-ATPase / proton pump
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / Golgi lumen acidification / Transferrin endocytosis and recycling / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane ...proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / Golgi lumen acidification / Transferrin endocytosis and recycling / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / Amino acids regulate mTORC1 / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / ROS and RNS production in phagocytes / protein localization to cilium / vacuolar acidification / proton transmembrane transporter activity / microvillus / cilium assembly / regulation of macroautophagy / specific granule membrane / ATP metabolic process / H+-transporting two-sector ATPase / ruffle / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / secretory granule / cilium / synaptic vesicle membrane / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / endosome membrane / apical plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #3240 / ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily ...Helix Hairpins - #3240 / ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 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 barrel-sandwich domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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 / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit F / Type IV secretion protein Dot / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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
Revision 1.2Mar 31, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource ...em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / entity_src_nat / pdbx_struct_sheet_hbond / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific ..._entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: V-type proton ATPase catalytic subunit A
B: V-type proton ATPase catalytic subunit A
C: V-type proton ATPase catalytic subunit A
D: V-type proton ATPase subunit B, brain isoform
E: V-type proton ATPase subunit B, brain isoform
F: V-type proton ATPase subunit B, brain isoform
X: SidK
Y: SidK
Z: SidK
J: V-type proton ATPase subunit E 1
M: V-type proton ATPase subunit G 1
G: V-type proton ATPase subunit D
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
N: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,36218
Polymers732,93517
Non-polymers4271
Water00
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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Protein , 2 types, 6 molecules ABCXYZ

#1: 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
#3: Protein SidK


Mass: 65505.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / References: UniProt: Q5ZWW6

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V-type proton ATPase subunit ... , 5 types, 11 molecules DEFJIHMLKGN

#2: 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
#4: 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
#5: 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
#6: 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
#7: 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

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ADP / ADENOSINE-5'-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

Component
IDNameTypeEntity IDParent-IDSource
1Human V-ATPase and SidK complexCOMPLEX#1-#70MULTIPLE SOURCES
2Human V-ATPaseCOMPLEX#1-#2, #4-#71NATURAL
3SidKCOMPLEX#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Legionella pneumophila subsp. pneumophila (bacteria)272624
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 FIELD
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00641368
ELECTRON MICROSCOPYf_angle_d0.63955859
ELECTRON MICROSCOPYf_dihedral_angle_d16.5165640
ELECTRON MICROSCOPYf_chiral_restr0.0476276
ELECTRON MICROSCOPYf_plane_restr0.0057255

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