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- EMDB-8724: Yeast V-ATPase in complex with Legionella pneumophila effector Si... -

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Basic information

Entry
Database: EMDB / ID: EMD-8724
TitleYeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)
Map dataV-ATPase:SidK complex, rotational state 1
SampleSidK != V-ATPase:SidK complex

SidK

  • Complex: V-ATPase:SidK complex
    • Protein or peptide: x 16 types
  • Complex: V-ATPase
  • Complex: SidK
KeywordsV-ATPase / SidK / rotational state 1 / HYDROLASE
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / polyphosphate metabolic process / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / polyphosphate metabolic process / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / pexophagy / protein targeting to vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuole organization / fungal-type vacuole / vacuolar acidification / intron homing / cellular hyperosmotic response / protein metabolic process / intein-mediated protein splicing / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / intracellular calcium ion homeostasis / cytoplasmic stress granule / endocytosis / ATPase binding / protein-containing complex assembly / endonuclease activity / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / 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 C ...Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / 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 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 / Intein / 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 / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / 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 / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / 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 / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / 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
: / V-type proton ATPase subunit B / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit D ...: / V-type proton ATPase subunit B / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit D / V-type proton ATPase subunit c' / V-type proton ATPase subunit F / V-type proton ATPase subunit H / V-type proton ATPase subunit G / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsZhao J
Funding support Canada, United States, 5 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI103168 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI10571 United States
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-05372 Canada
CitationJournal: PLoS Pathog / Year: 2017
Title: Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein.
Authors: Jianhua Zhao / Ksenia Beyrakhova / Yao Liu / Claudia P Alvarez / Stephanie A Bueler / Li Xu / Caishuang Xu / Michal T Boniecki / Voula Kanelis / Zhao-Qing Luo / Miroslaw Cygler / John L Rubinstein /
Abstract: Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector ...Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the 'open' conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK.
History
DepositionMay 3, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJun 21, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vox
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8724.png

Downloads & links

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Map

FileDownload / File: emd_8724.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV-ATPase:SidK complex, rotational state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.059364706 - 0.16670267
Average (Standard dev.)0.00085099 (±0.010817942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0590.1670.001

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Supplemental data

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Sample components

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Entire : SidK

EntireName: SidK
Components
  • Complex: V-ATPase:SidK complex
    • Protein or peptide: V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit C
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit c'
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: V-type proton ATPase subunit f
    • Protein or peptide: effector protein SidK
  • Complex: V-ATPase
  • Complex: SidK

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Supramolecule #1: V-ATPase:SidK complex

SupramoleculeName: V-ATPase:SidK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: V-ATPase

SupramoleculeName: V-ATPase / type: complex / ID: 2 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Supramolecule #3: SidK

SupramoleculeName: SidK / type: complex / ID: 3 / Parent: 0 / Macromolecule list: #16
Source (natural)Organism: Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Strain: ATCC 43290

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Macromolecule #1: V-type proton ATPase catalytic subunit A,V-type proton ATPase cat...

MacromoleculeName: V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 67.796508 KDa
SequenceString: MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI ...String:
MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI SSHKILLPPR SRGTITWIAP AGEYTLDEKI LEVEFDGKKS DFTLYHTWPV RVPRPVTEKL SADYPLLTGQ RV LDALFPC VQGGTTCIPG AFGCGKTVIS QSLSKYSNSD AIIYVGCGER GNEMAEVLME FPELYTEMSG TKEPIMKRTT LVA NTSNMP VAAREASIYT GITLAEYFRD QGKNVSMIAD SSSRWAEALR EISGRLGEMP ADQGFPAYLG AKLASFYERA GKAV ALGSP DRTGSVSIVA AVSPAGGDFS DPVTTATLGI TQVFWGLDKK LAQRKHFPSI NTSVSYSKYT NVLNKFYDSN YPEFP VLRD RMKEILSNAE ELEQVVQLVG KSALSDSDKI TLDVATLIKE DFLQQNGYST YDAFCPIWKT FDMMRAFISY HDEAQK AVA NGANWSKLAD STGDVKHAVS SSKFFEPSRG EKEVHGEFEK LLSTMQERFA ESTD

UniProtKB: V-type proton ATPase catalytic subunit A, V-type proton ATPase catalytic subunit A

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Macromolecule #2: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.815023 KDa
SequenceString: MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ ...String:
MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ KIPIFSASGL PHNEIAAQIC RQAGLVRPTK DVHDGHEENF SIVFAAMGVN LETARFFKQD FEENGSLERT SL FLNLAND PTIERIITPR LALTTAEYLA YQTERHVLTI LTDMSSYADA LREVSAAREE VPGRRGYPGY MYTDLSTIYE RAG RVEGRN GSITQIPILT MPNDDITHPI PDLTGYITEG QIFVDRQLHN KGIYPPINVL PSLSRLMKSA IGEGMTRKDH GDVS NQLYA KYAIGKDAAA MKAVVGEEAL SIEDKLSLEF LEKFEKTFIT QGAYEDRTVF ESLDQAWSLL RIYPKEMLNR ISPKI LDEF YDRARDDADE DEEDPDTRSS GKKKDASQEE SLI

UniProtKB: V-type proton ATPase subunit B

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Macromolecule #3: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.508393 KDa
SequenceString: MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP ...String:
MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP LEEIVISNDY LNKDLVSGGV VVSNASDKIE INNTLEERLK LLSEEALPAI RLELYGPSKT RKFFD

UniProtKB: V-type proton ATPase subunit E

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Macromolecule #4: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.738706 KDa
SequenceString:
MSQKNGIATL LQAEKEAHEI VSKARKYRQD KLKQAKTDAA KEIDSYKIQK DKELKEFEQK NAGGVGELEK KAEAGVQGEL AEIKKIAEK KKDDVVKILI ETVIKPSAEV HINAL

UniProtKB: V-type proton ATPase subunit G

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Macromolecule #5: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 29.235023 KDa
SequenceString: MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR ...String:
MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR RVNAIEHVII PRTENTIAYI NSELDELDRE EFYRLKKVQE KKQNETAKLD AEMKLKRDRA EQDASEVAAD EE PQGETLV ADQEDDVIF

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #6: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.47917 KDa
SequenceString:
MAEKRTLIAV IADEDTTTGL LLAGIGQITP ETQEKNFFVY QEGKTTKEEI TDKFNHFTEE RDDIAILLIN QHIAENIRAR VDSFTNAFP AILEIPSKDH PYDPEKDSVL KRVRKLFGE

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #7: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 44.241352 KDa
SequenceString: MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG ...String:
MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG DLSVRSLHDI VKPEDFVLNS EHLTTVLVAV PKSLKSDFEK SYETLSKNVV PASASVIAED AEYVLFNVHL FK KNVQEFT TAAREKKFIP REFNYSEELI DQLKKEHDSA ASLEQSLRVQ LVRLAKTAYV DVFINWFHIK ALRVYVESVL RYG LPPHFN IKIIAVPPKN LSKCKSELID AFGFLGGNAF MKDKKGKINK QDTSLHQYAS LVDTEYEPFV MYIINL

UniProtKB: V-type proton ATPase subunit C

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Macromolecule #8: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.482609 KDa
SequenceString: MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN ...String:
MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN NLINILQNIE QMDTCYVCIR LLQELAVIPE YRDVIWLHEK KFMPTLFKIL QRATDSQLAT RIVATNSNHL GI QLQYHSL LLIWLLTFNP VFANELVQKY LSDFLDLLKL VKITIKEKVS RLCISIILQC CSTRVKQHKK VIKQLLLLGN ALP TVQSLS ERKYSDEELR QDISNLKEIL ENEYQELTSF DEYVAELDSK LLCWSPPHVD NGFWSDNIDE FKKDNYKIFR QLIE LLQAK VRNGDVNAKQ EKIIIQVALN DITHVVELLP ESIDVLDKTG GKADIMELLN HSDSRVKYEA LKATQAIIGY TFK

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #9: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.822484 KDa
SequenceString: MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT ...String:
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT AEELDDMNIE IIRNKLYKAY LEDFYNFVTE EIPEPAKECM QTLLGFEADR RSINIALNSL QSSDIDPDLK SD LLPNIGK LYPLATFHLA QAQDFEGVRA ALANVYEYRG FLETGNLEDH FYQLEMELCR DAFTQQFAIS TVWAWMKSKE QEV RNITWI AECIAQNQRE RINNYISVY

UniProtKB: V-type proton ATPase subunit d

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Macromolecule #10: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.610641 KDa
SequenceString: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...String:
MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ

UniProtKB: V-type proton ATPase subunit c''

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Macromolecule #11: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.046361 KDa
SequenceString:
MSTQLASNIY APLYAPFFGF AGCAAAMVLS CLGAAIGTAK SGIGIAGIGT FKPELIMKSL IPVVMSGILA IYGLVVAVLI AGNLSPTED YTLFNGFMHL SCGLCVGFAC LSSGYAIGMV GDVGVRKYMH QPRLFVGIVL ILIFSEVLGL YGMIVALILN T RGSE

UniProtKB: V-type proton ATPase subunit c'

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Macromolecule #12: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 12 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.357501 KDa
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV C

UniProtKB: V-type proton ATPase subunit c

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Macromolecule #13: V-type proton ATPase subunit a, vacuolar isoform

MacromoleculeName: V-type proton ATPase subunit a, vacuolar isoform / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 95.625484 KDa
SequenceString: MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM ...String:
MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM IDANGENIAA AIGASVNYVT GVIARDKVAT LEQILWRVLR GNLFFKTVEI EQPVYDVKTR EYKHKNAFIV FS HGDLIIK RIRKIAESLD ANLYDVDSSN EGRSQQLAKV NKNLSDLYTV LKTTSTTLES ELYAIAKELD SWFQDVTREK AIF EILNKS NYDTNRKILI AEGWIPRDEL ATLQARLGEM IARLGIDVPS IIQVLDTNHT PPTFHRTNKF TAGFQSICDC YGIA QYREI NAGLPTIVTF PFMFAIMFGD MGHGFLMTLA ALSLVLNEKK INKMKRGEIF DMAFTGRYII LLMGVFSMYT GFLYN DIFS KTMTIFKSGW KWPDHWKKGE SITATSVGTY PIGLDWAWHG TENALLFSNS YKMKLSILMG FIHMTYSYFF SLANHL YFN SMIDIIGNFI PGLLFMQGIF GYLSVCIVYK WAVDWVKDGK PAPGLLNMLI NMFLSPGTID DELYPHQAKV QVFLLLM AL VCIPWLLLVK PLHFKFTHKK KSHEPLPSTE ADASSEDLEA QQLISAMDAD DAEEEEVGSG SHGEDFGDIM IHQVIHTI E FCLNCVSHTA SYLRLWALSL AHAQLSSVLW TMTIQIAFGF RGFVGVFMTV ALFAMWFALT CAVLVLMEGT SAMLHSLRL HWVESMSKFF VGEGLPYEPF AFEYKDMEVA VASASSSASS

UniProtKB: V-type proton ATPase subunit a, vacuolar isoform

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Macromolecule #14: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.387065 KDa
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE FAE

UniProtKB: V-type proton ATPase subunit e

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Macromolecule #15: V-type proton ATPase subunit f

MacromoleculeName: V-type proton ATPase subunit f / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.613678 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #16: effector protein SidK

MacromoleculeName: effector protein SidK / type: protein_or_peptide / ID: 16 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Molecular weightTheoretical: 65.49032 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILL ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI ...String:
MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILL ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI TEDNEGINQL FKLGLHLLAM ANEKIDEQYH LFKGYVKDQP EESPFEGILP AEDQKILVKT MIDYAMPKLS SK VLQDKLS ALSSSDVLTK TLLDSIDRIV KENEKLNALS KVKLGKFGLD IREIEVIYSQ ALKISPQDAL QYTAQQCDAQ LLS MAFPDS QNYIIESISN KKVKTIAELI HSKEFIYQII KTEVFKQVDP NEKIRLQAAT ELYQLLGRIM DKQINLFTKM NLEQ INEYI QTKTKAILDK IPERVELLTF MGFEIPTFKG IETLMTDISH SQDNETLAIA QEFYTNIKNA KNQLLGDKLI EDITP QDVE KFFNQCSQYG SEAAEKLADN RPVLTKIADI LTAIARWAIS LIGFNTPPQF LAPTRTCVDQ VSDEITKIKL KLEDTL GSL QKVQEESLSL

UniProtKB: UNIPROTKB: G8UUS6

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23924

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