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- PDB-7uwa: Citrus V-ATPase State 1, H in contact with subunits AB -

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Basic information

Entry
Database: PDB / ID: 7uwa
TitleCitrus V-ATPase State 1, H in contact with subunits AB
Components
  • (V-type proton ATPase subunit ...) x 14
  • V-type proton ATPase catalytic subunit A
KeywordsMEMBRANE PROTEIN / V-ATPase / rotary ATPase / complex
Function / homology
Function and homology information


proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / vacuole / vacuolar membrane / ATP metabolic process ...proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / vacuole / vacuolar membrane / ATP metabolic process / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATPase, V1 complex, subunit A / 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, V1 complex, subunit A / 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 / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit G / V-type proton ATPase subunit F / V-type proton ATPase subunit e1 / V-type proton ATPase subunit D / Vacuolar proton pump subunit B / V-type proton ATPase subunit C / V-type proton ATPase subunit c1 / Vacuolar membrane ATPase subunit c / V-type proton ATPase subunit E / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit a
Similarity search - Component
Biological speciesCitrus limon (lemon)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAbdelaziz, R.A. / Keon, K.A. / Schulze, W.X. / Schumacher, K. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2022
Title: Structure of V-ATPase from citrus fruit.
Authors: Yong Zi Tan / Kristine A Keon / Rana Abdelaziz / Peter Imming / Waltraud Schulze / Karin Schumacher / John L Rubinstein /
Abstract: We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, ...We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: V-type proton ATPase catalytic subunit A
F: V-type proton ATPase subunit B2
A: V-type proton ATPase catalytic subunit A
B: V-type proton ATPase subunit B2
C: V-type proton ATPase catalytic subunit A
D: V-type proton ATPase subunit B2
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
b: V-type proton ATPase subunit AP1 fragment
c: V-type proton ATPase subunit c"
d: V-type proton ATPase subunit d2
g: V-type proton ATPase subunit c
h: V-type proton ATPase subunit c
i: V-type proton ATPase subunit c
j: V-type proton ATPase subunit c
k: V-type proton ATPase subunit c
l: V-type proton ATPase subunit c
m: V-type proton ATPase subunit c
n: V-type proton ATPase subunit c
o: V-type proton ATPase subunit c
r: V-type proton ATPase subunit AP2 fragment
G: V-type proton ATPase subunit E
H: V-type proton ATPase subunit G
I: V-type proton ATPase subunit E
J: V-type proton ATPase subunit G
K: V-type proton ATPase subunit E
L: V-type proton ATPase subunit G
O: V-type proton ATPase subunit C
a: V-type proton ATPase subunit a3
e: V-type proton ATPase subunit e1
P: V-type proton ATPase subunit H


Theoretical massNumber of molelcules
Total (without water)937,23231
Polymers937,23231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 3 molecules EAC

#1: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar proton pump subunit alpha


Mass: 68755.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon)
References: UniProt: Q9SM09, H+-transporting two-sector ATPase

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V-type proton ATPase subunit ... , 14 types, 28 molecules FBDMNbcdghijklmnorGIKHJLOaeP

#2: Protein V-type proton ATPase subunit B2 / Vacuolar proton pump subunit B / V-ATPase subunit B / Vacuolar proton pump subunit B


Mass: 54417.594 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067FXK2
#3: Protein V-type proton ATPase subunit D


Mass: 29235.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067FFQ8
#4: Protein V-type proton ATPase subunit F


Mass: 14301.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067E4V9
#5: Protein/peptide V-type proton ATPase subunit AP1 fragment


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon)
#6: Protein V-type proton ATPase subunit c" / Vacuolar membrane ATPase subunit c


Mass: 18581.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: Q84V02
#7: Protein V-type proton ATPase subunit d2


Mass: 40693.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon)
#8: Protein
V-type proton ATPase subunit c / V-type proton ATPase subunit c1 / V-ATPase subunit c1 / V-type proton ATPase 16 kDa proteolipid ...V-type proton ATPase subunit c1 / V-ATPase subunit c1 / V-type proton ATPase 16 kDa proteolipid subunit c1 / V-ATPase 16 kDa proteolipid subunit c1 / Vacuolar H(+)-ATPase subunit c isoform 1 / Vacuolar proton pump 16 kDa proteolipid subunit c1 / Vacuolar proton pump subunit c1


Mass: 16581.588 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: P0DH92
#9: Protein/peptide V-type proton ATPase subunit AP2 fragment


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon)
#10: Protein V-type proton ATPase subunit E / V-ATPase subunit E / Vacuolar proton pump subunit E


Mass: 26331.332 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: Q9MB46
#11: Protein V-type proton ATPase subunit G


Mass: 12354.938 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067DRZ4
#12: Protein V-type proton ATPase subunit C


Mass: 42498.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A2H5Q4L7
#13: Protein V-type proton ATPase subunit a3 / V-type proton ATPase subunit a


Mass: 92939.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: V4UBK8
#14: Protein V-type proton ATPase subunit e1


Mass: 7757.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067F7P5
#15: Protein V-type proton ATPase subunit H


Mass: 51609.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon)

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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: Citrus V-ATPase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Citrus limon (lemon)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3414.211 nm / Nominal defocus min: 677.558 nm
Image recordingElectron dose: 31 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51571 / Symmetry type: POINT

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