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- EMDB-26388: Structure of porcine kidney V-ATPase with SidK, Rotary State 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-26388
TitleStructure of porcine kidney V-ATPase with SidK, Rotary State 3
Map dataMap used for model building.
Sample
  • Complex: Porcine kidney V-ATPase with SidK, Rotary State 3
    • Protein or peptide: x 17 types
  • Ligand: x 1 types
Keywordsproton translocation / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Insulin receptor recycling / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain ...ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Insulin receptor recycling / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / endosome to plasma membrane protein transport / clathrin-coated vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / osteoclast development / dendritic spine membrane / regulation of cellular pH / vacuolar membrane / microvillus / ATPase activator activity / autophagosome membrane / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / small GTPase binding / synaptic vesicle membrane / melanosome / presynapse / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / lysosome / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / 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-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 / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit D / Renin receptor / V-type proton ATPase 21 kDa proteolipid subunit isoform 1 / Ribonuclease kappa / V-type proton ATPase subunit a / V-type proton ATPase subunit / V-type proton ATPase subunit / V-type proton ATPase subunit G / V-type proton ATPase proteolipid subunit / Vacuolar proton pump subunit B ...V-type proton ATPase subunit D / Renin receptor / V-type proton ATPase 21 kDa proteolipid subunit isoform 1 / Ribonuclease kappa / V-type proton ATPase subunit a / V-type proton ATPase subunit / V-type proton ATPase subunit / V-type proton ATPase subunit G / V-type proton ATPase proteolipid subunit / Vacuolar proton pump subunit B / V-type proton ATPase subunit C / V-type proton ATPase subunit F / ATPase H+ transporting accessory protein 1 / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / Type IV secretion protein Dot / V-type proton ATPase subunit H
Similarity search - Component
Biological speciesSus scrofa (pig) / Legionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTan YZ
Funding support Canada, Singapore, 4 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
Canadian Institutes of Health Research (CIHR)FDN-143202 Canada
Canadian Institutes of Health Research (CIHR)FDN-143301 Canada
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Life Sci Alliance / Year: 2022
Title: CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7.
Authors: Yong Zi Tan / Yazan M Abbas / Jing Ze Wu / Di Wu / Kristine A Keon / Geoffrey G Hesketh / Stephanie A Bueler / Anne-Claude Gingras / Carol V Robinson / Sergio Grinstein / John L Rubinstein /
Abstract: V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins ...V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7's TLDc domain interacts with V-ATPase's stator, whereas its C-terminal α helix binds V-ATPase's rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme's activity.
History
DepositionMar 9, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26388.png

Downloads & links

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Map

FileDownload / File: emd_26388.map.gz / Format: CCP4 / Size: 13.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap used for model building.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.53 Å/pix.
x 201 pix.
= 307.129 Å		1.53 Å/pix.
x 141 pix.
= 215.449 Å		1.53 Å/pix.
x 121 pix.
= 184.889 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.52801 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-0.38918403 - 2.798913
Average (Standard dev.)0.16040607 (±0.25359786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions141121201
Spacing121141201
CellA: 184.88861 Å / B: 215.4487 Å / C: 307.129 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: V-ATPase with SidK, Rotary State 3

Fileemd_26388_additional_1.map
AnnotationV-ATPase with SidK, Rotary State 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Half map: V-ATPase with SidK, Rotary State 3

Fileemd_26388_half_map_1.map
AnnotationV-ATPase with SidK, Rotary State 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: V-ATPase with SidK, Rotary State 3

Fileemd_26388_half_map_2.map
AnnotationV-ATPase with SidK, Rotary State 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Porcine kidney V-ATPase with SidK, Rotary State 3

EntireName: Porcine kidney V-ATPase with SidK, Rotary State 3
Components
  • Complex: Porcine kidney V-ATPase with SidK, Rotary State 3
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: Vacuolar proton pump subunit B
    • Protein or peptide: V-type proton ATPase subunit C
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: Bacterial effector protein SidK
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit a
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit isoform 1
    • Protein or peptide: ATPase H+ transporting accessory protein 1
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase proteolipid subunit
    • Protein or peptide: ATPase H(+)-transporting lysosomal accessory protein 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Porcine kidney V-ATPase with SidK, Rotary State 3

SupramoleculeName: Porcine kidney V-ATPase with SidK, Rotary State 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Sus scrofa (pig)

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

MacromoleculeName: 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: Sus scrofa (pig)
Molecular weightTheoretical: 68.393844 KDa
SequenceString: MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DVKWEFTPSK NLRVGSHITG GDIYGIVNEN S LIKHRIML ...String:
MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DVKWEFTPSK NLRVGSHITG GDIYGIVNEN S LIKHRIML PPRNRGTVTY IAPPGNYDTS DVVLELEFEG VKEKFSMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERVNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MANSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVT IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM IAFYDLARRA VETTAQ SDN KITWSIIREH MGEILYKLSS MKFKDPVKDG EAKIKADYAQ LLEDVQNAFR SLED

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #2: Vacuolar proton pump subunit B

MacromoleculeName: Vacuolar proton pump subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 57.162859 KDa
SequenceString: MAMKVDSRPG GLPSSGSHLG TAREHVQAVT RNYITHPRVT YRTVCSVNGP LVVLDHVKFA QYAEIVNFTL PNGTQRSGQV LEVSGTKAI VQVFEGTSGI DAQKTTCEFT GDILRTPVSE DMLGRVFNGS GKPIDNGPVV MAEDFLDING QPINPHDRIY P EEMIQTGI ...String:
MAMKVDSRPG GLPSSGSHLG TAREHVQAVT RNYITHPRVT YRTVCSVNGP LVVLDHVKFA QYAEIVNFTL PNGTQRSGQV LEVSGTKAI VQVFEGTSGI DAQKTTCEFT GDILRTPVSE DMLGRVFNGS GKPIDNGPVV MAEDFLDING QPINPHDRIY P EEMIQTGI SPIDVMNSIA RGQKIPIFSA AGLPHNEIAA QICRQAGLVK KSKAVLDYDD DNFAIVFAAM GVNMETARFF KS DFEENGT MGNVCLFLNL ANDPTIERII TPRLALTTAE FLAYQCEKHV LVILTDMSSY AEALREVSAA REEVPGRRGF PGY MYTDLA TIYERAGRVE GRGGSITQIP ILTMPNDDIT HPIPDLTGFI TEGQIYVDRQ LHNRQIYPPI NVLPSLSRLM KSAI GEGMT RKDHGDVSNQ LYACYAIGKD VQAMKAVVGE EALTSEDLLY LEFLQKFERN FINQGPYEKR SVFESLDLGW KLLRI FPKE MLKRIPQSMI DEFYSREGAP QDPEPEPDTA L

UniProtKB: Vacuolar proton pump subunit B

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Macromolecule #3: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 44.066566 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLALTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSRDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLALTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSRDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE IVKKDDFVLD SEYLVTLLVV VPKLNHNDWI KQYETLAEMV VPRSSNVLSE DQDSYLCNVT LFRKAVDDFR HK ARENKFI VRDFQYNEEE MKADKEEMNR LSTDKKKQFG PLVRWLKVNF SEAFIAWIHV KALRVFVESV LRYGLPVNFQ AML LQPNKK TMKKLREVLY ELYKHLDSSA AAIIDAPVDI PGLNLSQQEY YPYVYYKIDC NLLEFK

UniProtKB: V-type proton ATPase subunit C

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Macromolecule #4: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 28.301902 KDa
SequenceString: MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR ...String:
MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR VNAIEHVIIP RIERTLAYII TELDEREREE FYRLKKIQEK KKILKEKSEK DLEQRRAAGE AMEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #5: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 26.162373 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLGKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPVYKIAT K RDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLGKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPVYKIAT K RDVDVQID QEAYLPEEIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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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: Sus scrofa (pig)
Molecular weightTheoretical: 13.403288 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRED IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA KGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #7: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.748474 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSHGSCS TEVEKDTQEK MTILQTYFR QNRDEVLDNL LAFVCDIRPE IHENYRING

UniProtKB: V-type proton ATPase subunit G

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Macromolecule #8: Bacterial effector protein SidK

MacromoleculeName: Bacterial effector protein SidK / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 38.539371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI ...String:
MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ 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 K

UniProtKB: Type IV secretion protein Dot

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Macromolecule #9: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 55.917797 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISSEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD TLQENHQRVS IFFDYAKRSK NTAWSYFLPM LNRQDLFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISSEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD TLQENHQRVS IFFDYAKRSK NTAWSYFLPM LNRQDLFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLASQKLR GSGVAVETGT VSSSDSSQYV QCVAGCLQLM LRVNEYRFAW VEADGVNCIM GVLSNKCGFQ LQ YQMIFSI WLLAFSPQMC EHLRRYNIIP VLSDILQESV KEKVTRIILA AFRNFLEKST ERETRQEYAL ALIQCKVLKQ LEN LEQQKY DDEDISEDIK FLLEKLGESV QDLSSFDEYS SELKSGRLEW SPVHKSEKFW RENAVRLNEK NYELLKILTK LLEV SDDPQ VLAVAAHDVG EYVRHYPRGK RVIEQLGGKQ LVMNHMHHED QQVRYNALLA VQKLMVHNWE YLGKQLQSEQ PQTAA ARS

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #10: V-type proton ATPase subunit a

MacromoleculeName: V-type proton ATPase subunit a / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 96.365258 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGTPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGTPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTCGFQN IVDAYGIGTY REINPAPYTI ITFP FLFAV MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSTVFS GRYIILLMGI FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FDGYNWTEET LRGNPVLQLN PAVLGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMMFGVS LSLFNH IYF KRPLNIYFGF IPEIIFMTSL FGYLVILIFY KWTAYDAQTS EKAPSLLIHF INMFLFSYGD SGNSMLYSGQ KGIQCFL VV VALLCVPWML LIKPLVLRHQ YLRRKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLSVKSLA GGLALFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYSGTG FKFLPFSFEH IREGKFDE

UniProtKB: V-type proton ATPase subunit a

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Macromolecule #11: V-type proton ATPase 21 kDa proteolipid subunit isoform 1

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit isoform 1
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.530426 KDa
SequenceString: MTGLVLLYSG VFVAFWACLL VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLVLLYSG VFVAFWACLL VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

UniProtKB: V-type proton ATPase 21 kDa proteolipid subunit isoform 1

+
Macromolecule #12: ATPase H+ transporting accessory protein 1

MacromoleculeName: ATPase H+ transporting accessory protein 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 51.547465 KDa
SequenceString: MMAAAAAARV RAGTRRGPAL WQMPWLPLVA VAVVAAASAA EQQVPLVLWS SDRNLWAPAA NTHEGHITSD RQLSTYLDPA LELGPRNVL LFLQDKLSVE DFTAYGGVFG NKQDSAFSNL ENALDLAPSS LVLPAVDWYA VSTLTTYLQE KLGASPLHVD L ATLRELKL ...String:
MMAAAAAARV RAGTRRGPAL WQMPWLPLVA VAVVAAASAA EQQVPLVLWS SDRNLWAPAA NTHEGHITSD RQLSTYLDPA LELGPRNVL LFLQDKLSVE DFTAYGGVFG NKQDSAFSNL ENALDLAPSS LVLPAVDWYA VSTLTTYLQE KLGASPLHVD L ATLRELKL NASLPALLLI RLPYTASSGL MAPKEVLTAN DEVIGQVLST LKSEEVPYTA ALTAVRPSRV ARDVAMVAGG LG RQLLQRP SASAATHPPV SYNDTAPRIL FWAQNFSVAY GGRWEDLTSL TFGVQDLNLT GSFWNDSVAW LALTYDQLFG TMV TFKFIL ANRFYQVSAR HWFTLERLEI HSNGSIASFN ASQVTGPSIY SFHCEYVNSH NKNGDLLVPS TQPSLWQLTF QDFQ IQAFN VTGERFSYAS DCAGFFSPGI WMGLLTSLFM LFIFTYGLHM ILGLKTMDRF DDHKGPTIAL TQIV

UniProtKB: ATPase H+ transporting accessory protein 1

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Macromolecule #13: V-type proton ATPase subunit

MacromoleculeName: V-type proton ATPase subunit / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 40.369949 KDa
SequenceString: MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDRLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI ...String:
MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDRLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI SEQDLDEMNI EIIRNTLYKA YLESFYKFCT LLGGTTADAM CPILEFEADR RAFIITINSF GTELSKEDRA KL FPHCGRL YPEGLAQLAR ADDYEQVKNV ADYYPEYKLL FEGAGSNPGD KTLEDRFFEH EVKLNKLAFL NQFHFGVFYA FVK LKEQEC RNIVWIAECI AQRHRAKIDN YIPIF

UniProtKB: V-type proton ATPase subunit

+
Macromolecule #14: V-type proton ATPase subunit

MacromoleculeName: V-type proton ATPase subunit / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.343286 KDa
SequenceString:
MAYTGLTVPL IVMSVFWGFV GFLVPWFIPK GPNRGVIITM LVTCSVCCYL FWLIAILAQL NPLFGPQLKN ETIWYLKYHW P

UniProtKB: V-type proton ATPase subunit

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Macromolecule #15: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 11.016065 KDa
SequenceString:
MASLLCCGPK LAACGIVLSA WGVIMLIMLG IFFNVHSAVL IEDVPFTEKD FENGPQDIYK LYEQVSYNCF IAAGLYLLLG GFSFCQVRL NKRKEYMVR

UniProtKB: Ribonuclease kappa

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Macromolecule #16: V-type proton ATPase proteolipid subunit

MacromoleculeName: V-type proton ATPase proteolipid subunit / type: protein_or_peptide / ID: 16 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 15.639677 KDa
SequenceString:
MSEAKSGPEY AAFFAVMGAS AAMVFSALGA AYGTAKSGTG IAAMSVMRPE LIMKSIIPVV MAGIIAIYGL VVAVLIANSL TEGISLYKS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

UniProtKB: V-type proton ATPase proteolipid subunit

+
Macromolecule #17: ATPase H(+)-transporting lysosomal accessory protein 2

MacromoleculeName: ATPase H(+)-transporting lysosomal accessory protein 2
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 39.200055 KDa
SequenceString: MAVLVALLSL VVAGVLGNEF SILRSPGSVV FRDGNWPIPG ERIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATVMVM VKGVDKLAL PPGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRSRL F QENSILSL ...String:
MAVLVALLSL VVAGVLGNEF SILRSPGSVV FRDGNWPIPG ERIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATVMVM VKGVDKLAL PPGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRSRL F QENSILSL LPLNSLSRNN EVDLLFLSEL QVLHDISSLL SRHKHLAKDH SPDLYSLELA GLDEIGKRYG EDSEQFRDAS KI LVDALQK FADDMYNLYG GNAVVELVTV RSFDTSLVRK TRTILEAKQV KDPPSPYNLA YKYNVDYPVV FNMILWIMIA LAL AVIITS YNIWNMDPGY DSIIYRMTNQ KIRMD

UniProtKB: Renin receptor

+
Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.911445 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: mEAK7 + V-ATPase + SidK model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22866
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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