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- EMDB-26622: The V1 region of bovine V-ATPase in complex with human mEAK7 (foc... -

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Basic information

Entry
Database: EMDB / ID: EMD-26622
TitleThe V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement)
Map data
Sample
  • Complex: Cryo-EM structure of the V1 region of bovine V-ATPase in complex with human mEAK7
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: KIAA1609 protein, isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: V-type proton ATPase subunit G
Keywordsproton transport / mTOR signaling
Function / homology
Function and homology information


ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / pH reduction / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / pH reduction / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / Neutrophil degranulation / microvillus / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / ruffle / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cilium / synaptic vesicle membrane / melanosome / intracellular iron ion homeostasis / lysosome / endosome / apical plasma membrane / lysosomal membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily ...TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / 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 / ATP synthase subunit D / 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 / 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 D / KIAA1609 protein, isoform CRA_a / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit G 2
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsWang R / Li X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135343 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL020948 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL072304 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis of mEAK7-mediated human V-ATPase regulation.
Authors: Rong Wang / Yu Qin / Xiao-Song Xie / Xiaochun Li /
Abstract: The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The ...The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The molecular basis of its regulation by an endogenous modulator without affecting V-ATPase assembly remains unclear. Here, we discover that a lysosome-anchored protein termed (mammalian Enhancer-of-Akt-1-7 (mEAK7)) binds to intact V-ATPase. We determine cryo-EM structure of human mEAK7 in complex with human V-ATPase in native lipid-containing nanodiscs. The structure reveals that the TLDc domain of mEAK7 engages with subunits A, B, and E, while its C-terminal domain binds to subunit D, presumably blocking V-V torque transmission. Our functional studies suggest that mEAK7, which may act as a V-ATPase inhibitor, does not affect the activity of V-ATPase in vitro. However, overexpression of mEAK7 in HCT116 cells that stably express subunit a4 of V-ATPase represses the phosphorylation of ribosomal protein S6. Thus, this finding suggests that mEAK7 potentially links mTOR signaling with V-ATPase activity.
History
DepositionApr 10, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26622.png

Downloads & links

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Map

FileDownload / File: emd_26622.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.04042345 - 0.0764316
Average (Standard dev.)0.00009773329 (±0.003705038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26622_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26622_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the V1 region of bovine V-ATPase in complex ...

EntireName: Cryo-EM structure of the V1 region of bovine V-ATPase in complex with human mEAK7
Components
  • Complex: Cryo-EM structure of the V1 region of bovine V-ATPase in complex with human mEAK7
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: KIAA1609 protein, isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: V-type proton ATPase subunit G

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Supramolecule #1: Cryo-EM structure of the V1 region of bovine V-ATPase in complex ...

SupramoleculeName: Cryo-EM structure of the V1 region of bovine V-ATPase in complex with human mEAK7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)

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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: Bos taurus (cattle)
Molecular weightTheoretical: 68.420914 KDa
SequenceString: MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DVKWDFTPCK NLRVGSHITG GDIYGIVNEN S LIKHKIML ...String:
MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DVKWDFTPCK NLRVGSHITG GDIYGIVNEN S LIKHKIML PPRNRGTVTY IAPPGNYDTS DVVLELEFEG IKEKFSMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERGNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MADSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVS IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM IAFYDMARRA VETTAQ SDN KITWSIIREH MGEILYKLSS MKFKDPVKDG EAKIKADYAQ LLEDMQNAFR SLED

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #2: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 28.297893 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 KKILKEKSDK DLEQRRAAGE VIEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #3: KIAA1609 protein, isoform CRA_a

MacromoleculeName: KIAA1609 protein, isoform CRA_a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.982465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGN SRSRVGRSFC SQFLPEEQAE IDQLFDALSS DKNSPNVSSK SFSLKALQNH VGEALPPEMV TRLYDGMRRV DLTGKAKGP SENVSQEQFT ASMSHLLKGN SEEKSLMIMK MISATEGPVK AREVQKFTED LVGSVVHVLS HRQELRGWTG K EAPGPNPR ...String:
MGHHHHHHGN SRSRVGRSFC SQFLPEEQAE IDQLFDALSS DKNSPNVSSK SFSLKALQNH VGEALPPEMV TRLYDGMRRV DLTGKAKGP SENVSQEQFT ASMSHLLKGN SEEKSLMIMK MISATEGPVK AREVQKFTED LVGSVVHVLS HRQELRGWTG K EAPGPNPR VQVLAAQLLS DMKLQDGKRL LGPQWLDYDC DRAVIEDWVF RVPHVAIFLS VVICKGFLVL CSSLDLTTLV PE RQVDQGR GFESILDVLS VMYINAQLPR EQRHRWRLLF SSELHGHSFS QLCGHITHRG PCVAVLEDHD KHVFGGFASC SWE VKPQFQ GDNRCFLFSI CPSMAVYTHT GYNDHYMYLN HGQQTIPNGL GMGGQHNYFG LWVDVDFGKG HSRAKPTCTT YNSP QLSAQ ENFQFDKMEV WAVGDPSEEQ LAKGNKSILD ADPEAQALLE ISGHSRHSEG LREVPDDE

UniProtKB: KIAA1609 protein, isoform CRA_a

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Macromolecule #4: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 26.178371 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPVYKVAT K RDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPVYKVAT K RDVDVQID QEAYLPEEIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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Macromolecule #5: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 56.637555 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TSGPLAGSRE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TSGPLAGSRE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE MIQTGISAID GMNSIARGQK IPIFSAAGLP HNEIAAQICR QAGLVKKSKD VVDYSEENFA IVFAAMGVNM ET ARFFKSD FEENGSMDNV CLFLNLANDP TIERIITPRL ALTTAEFLAY QCEKHVLVIL TDMSSYAEAL REVSAAREEV PGR RGFPGY MYTDLATIYE RAGRVEGRNG SITQIPILTM PNDDITHPIP DLTGYITEGQ IYVDRQLHNR QIYPPINVLP SLSR LMKSA IGEGMTRKDH ADVSNQLYAC YAIGKDVQAM KAVVGEEALT SDDLLYLEFL QKFERNFIAQ GPYENRTVYE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

UniProtKB: V-type proton ATPase subunit B, brain isoform

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Macromolecule #6: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 13.588344 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVDQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLAQL LGMVCDVRPQ VHPNYRIAA

UniProtKB: V-type proton ATPase subunit G 2

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13841
FSC plot (resolution estimation)

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