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- EMDB-26623: CryoEM structure of a mEAK7 bound human V-ATPase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-26623
TitleCryoEM structure of a mEAK7 bound human V-ATPase complex
Map data
Sample
  • Complex: CryoEM structure of mEAK7 bound human V-ATPase complex
    • Protein or peptide: x 17 types
  • Ligand: x 3 types
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / synaptic vesicle lumen acidification ...proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / regulation of pH / proton-transporting V-type ATPase complex / ROS and RNS production in phagocytes / protein localization to cilium / Nef Mediated CD4 Down-regulation / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / azurophil granule membrane / autophagosome membrane / proton transmembrane transporter activity / microvillus / tertiary granule membrane / ATPase activator activity / ficolin-1-rich granule membrane / cilium assembly / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / transmembrane transporter complex / regulation of macroautophagy / specific granule membrane / enzyme regulator activity / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / Insulin receptor recycling / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / ossification / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / brush border membrane / sensory perception of sound / transmembrane transport / synaptic vesicle membrane / cilium / small GTPase binding / endocytosis / phagocytic vesicle membrane / melanosome / apical part of cell / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / membrane => GO:0016020 / Hydrolases; Acting on ester bonds / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / 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 ...TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / 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 / 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 / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Renin receptor / KIAA1609 protein, isoform CRA_a / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 ...Renin receptor / KIAA1609 protein, isoform CRA_a / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / V-type proton ATPase subunit F / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase 116 kDa subunit a 4 / V-type proton ATPase subunit H / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 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-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26623.png

Downloads & links

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Map

FileDownload / File: emd_26623.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.842 Å
Density
Contour LevelBy AUTHOR: 2.95
Minimum - Maximum-13.098031 - 23.5432
Average (Standard dev.)0.0040511023 (±1.0213506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 404.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoEM structure of mEAK7 bound human V-ATPase complex

EntireName: CryoEM structure of mEAK7 bound human V-ATPase complex
Components
  • Complex: CryoEM structure of mEAK7 bound human V-ATPase complex
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 4
    • Protein or peptide: KIAA1609 protein, isoform CRA_a
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • 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 G 1
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: V-type proton ATPase subunit e 1
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: ATPase H(+)-transporting lysosomal accessory protein 2
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: CryoEM structure of mEAK7 bound human V-ATPase complex

SupramoleculeName: CryoEM structure of mEAK7 bound human V-ATPase complex
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: V-type proton ATPase 116 kDa subunit a 4

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.530477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES LERILRFLED EMQNEIVVQL LEKSPLTPL PREMITLETV LEKLEGELQE ANQNQQALKQ SFLELTELKY LLKKTQDFFE TETNLADDFF TEDTSGLLEL K AVPAYMTG ...String:
MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES LERILRFLED EMQNEIVVQL LEKSPLTPL PREMITLETV LEKLEGELQE ANQNQQALKQ SFLELTELKY LLKKTQDFFE TETNLADDFF TEDTSGLLEL K AVPAYMTG KLGFIAGVIN RERMASFERL LWRICRGNVY LKFSEMDAPL EDPVTKEEIQ KNIFIIFYQG EQLRQKIKKI CD GFRATVY PCPERAVERR EMLESVNVRL EDLITVITQT ESHRQRLLQE AAANWHSWLI KVQKMKAVYH ILNMCNIDVT QQC VIAEIW FPVADATRIK RALEQGMELS GSSMAPIMTT VQSKTAPPTF NRTNKFTAGF QNIVDAYGVG SYREINPAPY TIIT FPFLF AVMFGDCGHG TVMLLAALWM ILNERRLLSQ KTDNEIWNTF FHGRYLILLM GIFSIYTGLI YNDCFSKSLN IFGSS WSVQ PMFRNGTWNT HVMEESLYLQ LDPAIPGVYF GNPYPFGIDP IWNLASNKLT FLNSYKMKMS VILGIVQMVF GVILSL FNH IYFRRTLNII LQFIPEMIFI LCLFGYLVFM IIFKWCCFDV HVSQHAPSIL IHFINMFLFN YSDSSNAPLY KHQQEVQ SF FVVMALISVP WMLLIKPFIL RASHRKSQLQ ASRIQEDATE NIEGDSSSPS SRSGQRTSAD THGALDDHGE EFNFGDVF V HQAIHTIEYC LGCISNTASY LRLWALSLAH AQLSEVLWTM VMNSGLQTRG WGGIVGVFII FAVFAVLTVA ILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE DYKDDDDKDY KDDDDK

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Macromolecule #2: KIAA1609 protein, isoform CRA_a

MacromoleculeName: KIAA1609 protein, isoform CRA_a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 51.096547 KDa
SequenceString: MGNSRSRVGR SFCSQFLPEE QAEIDQLFDA LSSDKNSPNV SSKSFSLKAL QNHVGEALPP EMVTRLYDGM RRVDLTGKAK GPSENVSQE QFTASMSHLL KGNSEEKSLM IMKMISATEG PVKAREVQKF TEDLVGSVVH VLSHRQELRG WTGKEAPGPN P RVQVLAAQ ...String:
MGNSRSRVGR SFCSQFLPEE QAEIDQLFDA LSSDKNSPNV SSKSFSLKAL QNHVGEALPP EMVTRLYDGM RRVDLTGKAK GPSENVSQE QFTASMSHLL KGNSEEKSLM IMKMISATEG PVKAREVQKF TEDLVGSVVH VLSHRQELRG WTGKEAPGPN P RVQVLAAQ LLSDMKLQDG KRLLGPQWLD YDCDRAVIED WVFRVPHVAI FLSVVICKGF LVLCSSLDLT TLVPERQVDQ GR GFESILD VLSVMYINAQ LPREQRHRWR LLFSSELHGH SFSQLCGHIT HRGPCVAVLE DHDKHVFGGF ASCSWEVKPQ FQG DNRCFL FSICPSMAVY THTGYNDHYM YLNHGQQTIP NGLGMGGQHN YFGLWVDVDF GKGHSRAKPT CTTYNSPQLS AQEN FQFDK MEVWAVGDPS EEQLAKGNKS ILDADPEAQA LLEISGHSRH SEGLREVPDD E

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Macromolecule #3: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: human (human)
Molecular weightTheoretical: 68.379875 KDa
SequenceString: MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML ...String:
MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML PPRNRGTVTY IAPPGNYDTS DVVLELEFEG VKEKFTMVQV 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 MGDILYKLSS MKFKDPLKDG EAKIKSDYAQ LLEDMQNAFR SLED

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Macromolecule #4: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 56.5615 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TGGPAVGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TGGPAVGARE 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 GPYENRTVFE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

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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: human (human)
Molecular weightTheoretical: 28.311918 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 VLEPANLLAE EK DEDLLFE

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Macromolecule #6: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 26.183346 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID QESYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

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Macromolecule #7: V-type proton ATPase subunit G 1

MacromoleculeName: V-type proton ATPase subunit G 1 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 13.781547 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSRGSCS TEVEKETQEK MTILQTYFR QNRDEVLDNL LAFVCDIRPE IHENYRING

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Macromolecule #8: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 13.38821 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQQSIPAVL EIPSKEHPYD AAKDSILRRA RGMFTAEDLR

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Macromolecule #9: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 43.9995 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATSKNN NLAVTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATSKNN NLAVTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE 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 TLKKLREVLH ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

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Macromolecule #10: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 55.949949 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHICKEQT VQYILTMVDD MLQENHQRVS IFFDYARCSK NTAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHICKEQT VQYILTMVDD MLQENHQRVS IFFDYARCSK NTAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLSSQKLR GSGVAVETGT VSSSDSSQYV QCVAGCLQLM LRVNEYRFAW VEADGVNCIM GVLSNKCGFQ LQ YQMIFSI WLLAFSPQMC EHLRRYNIIP VLSDILQESV KEKVTRIILA AFRNFLEKST ERETRQEYAL AMIQCKVLKQ LEN LEQQKY DDEDISEDIK FLLEKLGESV QDLSSFDEYS SELKSGRLEW SPVHKSEKFW RENAVRLNEK NYELLKILTK LLEV SDDPQ VLAVAAHDVG EYVRHYPRGK RVIEQLGGKQ LVMNHMHHED QQVRYNALLA VQKLMVHNWE YLGKQLQSEQ PQTAA ARS

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Macromolecule #11: V-type proton ATPase subunit d 1

MacromoleculeName: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
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

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Macromolecule #12: V-type proton ATPase subunit e 1

MacromoleculeName: V-type proton ATPase subunit e 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 9.380329 KDa
SequenceString:
MAYHGLTVPL IVMSVFWGFV GFLVPWFIPK GPNRGVIITM LVTCSVCCYL FWLIAILAQL NPLFGPQLKN ETIWYLKYHW P

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Macromolecule #13: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: human (human)
Molecular weightTheoretical: 15.43522 KDa
SequenceString:
MGWLRPGPRP LCPPARASWA FSHRFPSPLA PRRSPTPFFM ASLLCCGPKL AACGIVLSAW GVIMLIMLGI FFNVHSAVLI EDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRLN KRKEYMVR

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Macromolecule #14: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 52.06748 KDa
SequenceString: MMAAMATARV RMGPRCAQAL WRMPWLPVFL SLAAAAAAAA AEQQVPLVLW SSDRDLWAPA ADTHEGHITS DLQLSTYLDP ALELGPRNV LLFLQDKLSI EDFTAYGGVF GNKQDSAFSN LENALDLAPS SLVLPAVDWY AVSTLTTYLQ EKLGASPLHV D LATLRELK ...String:
MMAAMATARV RMGPRCAQAL WRMPWLPVFL SLAAAAAAAA AEQQVPLVLW SSDRDLWAPA ADTHEGHITS DLQLSTYLDP ALELGPRNV LLFLQDKLSI EDFTAYGGVF GNKQDSAFSN LENALDLAPS SLVLPAVDWY AVSTLTTYLQ EKLGASPLHV D LATLRELK LNASLPALLL IRLPYTASSG LMAPREVLTG NDEVIGQVLS TLKSEDVPYT AALTAVRPSR VARDVAVVAG GL GRQLLQK QPVSPVIHPP VSYNDTAPRI LFWAQNFSVA YKDQWEDLTP LTFGVQELNL TGSFWNDSFA RLSLTYERLF GTT VTFKFI LANRLYPVSA RHWFTMERLE VHSNGSVAYF NASQVTGPSI YSFHCEYVSS LSKKGSLLVA RTQPSPWQMM LQDF QIQAF NVMGEQFSYA SDCASFFSPG IWMGLLTSLF MLFIFTYGLH MILSLKTMDR FDDHKGPTIS LTQIV

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Macromolecule #15: ATPase H(+)-transporting lysosomal accessory protein 2

MacromoleculeName: ATPase H(+)-transporting lysosomal accessory protein 2
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 38.421098 KDa
SequenceString: MAVFVVLLAL VAGVLGNEFS ILKSPGSVVF RNGNWPIPGE RIPDVAALSM GFSVKEDLSW PGLAVGNLFH RPRATVMVMV KGVNKLALP PGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLSV TLRQLRNRLF Q ENSVLSSL ...String:
MAVFVVLLAL VAGVLGNEFS ILKSPGSVVF RNGNWPIPGE RIPDVAALSM GFSVKEDLSW PGLAVGNLFH RPRATVMVMV KGVNKLALP PGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLSV TLRQLRNRLF Q ENSVLSSL PLNSLSRNNE VDLLFLSELQ VLHDISSLHL AKDHSPDLYS LELAGLDEIG KRYGEDSEQF RDASKILVDA LQ KFADDMY SLYGGNAVVE LVTVKSFDTS LIRKTRTILE AKQAKNPASP YNLAYKYNFE YSVVFNMVLW IMIALALAVI ITS YNIWNM DPGYDSIIYR MTNQKIRMD

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Macromolecule #16: V-type proton ATPase 16 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit / type: protein_or_peptide / ID: 16 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 15.743655 KDa
SequenceString:
MSESKSGPEY ASFFAVMGAS AAMVFSALGA AYGTAKSGTG IAAMSVMRPE QIMKSIIPVV MAGIIAIYGL VVAVLIANSL NDDISLYKS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

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Macromolecule #17: V-type proton ATPase 21 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 21.418213 KDa
SequenceString: MTGLALLYSG VFVAFWACAL AVGVCYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLALLYSG VFVAFWACAL AVGVCYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

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Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 20 / 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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Macromolecule #21: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 21 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #22: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 22 / Number of copies: 9 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24984
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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