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

Basic information

Entry

Database: EMDB / ID: EMD-26623

• Title: CryoEM structure of a mEAK7 bound human V-ATPase complex

Sample

• Complex: CryoEM structure of mEAK7 bound human V-ATPase complex
  • Protein or peptide: x 17 types
• Ligand: x 3 types

• Keywords: proton transport / mTOR signaling

Function / homology

Function:

Blockage of phagosome acidification / proton-transporting two-sector ATPase complex / Ion channel transport / plasma membrane proton-transporting V-type ATPase complex / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / renal tubular secretion / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / Golgi lumen acidification / synaptic vesicle lumen acidification / vacuolar transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Transferrin endocytosis and recycling / cellular response to increased oxygen levels / vacuolar proton-transporting V-type ATPase, V1 domain / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / regulation of pH / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / osteoclast development / Nef Mediated CD4 Down-regulation / ROS and RNS production in phagocytes / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / azurophil granule membrane / microvillus / proton transmembrane transporter activity / ATPase activator activity / autophagosome membrane / tertiary granule membrane / ficolin-1-rich granule membrane / proton-transporting ATPase activity, rotational mechanism / cilium assembly / RHOA GTPase cycle / positive regulation of Wnt signaling pathway / regulation of macroautophagy / transporter activator activity / H+-transporting two-sector ATPase / ATP metabolic process / specific granule membrane / Insulin receptor recycling / enzyme regulator activity / ruffle / receptor-mediated endocytosis of virus by host cell / proton-transporting ATP synthase activity, rotational mechanism / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / ossification / secretory granule / brush border membrane / sensory perception of sound / small GTPase binding / transmembrane transport / phagocytic vesicle membrane / endocytosis / apical part of cell / synaptic vesicle membrane / melanosome / signaling receptor activity / ATPase binding / basolateral plasma membrane / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / early endosome / endosome / endosome membrane / cilium / apical plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol

Domain/homology:

: / TLDc domain / TLDc domain / TLDc domain profile. / 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 transmembrane spanning segment / Renin receptor N-terminal domain / 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 / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 barrel-sandwich domain / 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

Component:

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

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 4.08 Å
• Authors: Wang R / Li X

Funding support

United States, 3 items

Organization	Grant number	Country
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

• Citation: Journal: 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 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

Deposition	Apr 10, 2022	-
Header (metadata) release	Jun 15, 2022	-
Map release	Jun 15, 2022	-
Update	Oct 30, 2024	-
Current status	Oct 30, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_26623.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.842 Å

Density

Contour Level	By AUTHOR: 2.95
Minimum - Maximum	-13.098031000000001 - 23.543199999999999
Average (Standard dev.)	0.0040511023 (±1.0213506)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 480 480 480 Spacing 480 480 480
Cell	A=B=C: 404.16 Å α=β=γ: 90.0 °

Supplemental data

Sample components

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

• Entire: Name: 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

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

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

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

• Macromolecule: Name: 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 weight: Theoretical: 98.530477 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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

UniProtKB: V-type proton ATPase 116 kDa subunit a 4

Macromolecule #2: KIAA1609 protein, isoform CRA_a

• Macromolecule: Name: KIAA1609 protein, isoform CRA_a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 51.096547 KDa

Sequence

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

UniProtKB: KIAA1609 protein, isoform CRA_a

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

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 68.379875 KDa

Sequence

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

UniProtKB: V-type proton ATPase catalytic subunit A

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

• Macromolecule: Name: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 56.5615 KDa

Sequence

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

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

Macromolecule #5: V-type proton ATPase subunit D

• Macromolecule: Name: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 28.311918 KDa

Sequence

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

UniProtKB: V-type proton ATPase subunit D

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

• Macromolecule: Name: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 26.183346 KDa

Sequence

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

UniProtKB: V-type proton ATPase subunit E 1

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

• Macromolecule: Name: V-type proton ATPase subunit G 1 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.781547 KDa

Sequence

String:

MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSRGSCS TEVEKETQEK MTILQTYFR QNRDEVLDNL LAFVCDIRPE IHENYRING

UniProtKB: V-type proton ATPase subunit G 1

Macromolecule #8: V-type proton ATPase subunit F

• Macromolecule: Name: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.38821 KDa

Sequence

String:

MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQQSIPAVL EIPSKEHPYD AAKDSILRRA RGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

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

• Macromolecule: Name: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 43.9995 KDa

Sequence

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

UniProtKB: V-type proton ATPase subunit C 1

Macromolecule #10: V-type proton ATPase subunit H

• Macromolecule: Name: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 55.949949 KDa

Sequence

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

UniProtKB: V-type proton ATPase subunit H

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

• Macromolecule: Name: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 40.369949 KDa

Sequence

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 d 1

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

• Macromolecule: Name: V-type proton ATPase subunit e 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 9.380329 KDa

Sequence

String:

MAYHGLTVPL IVMSVFWGFV GFLVPWFIPK GPNRGVIITM LVTCSVCCYL FWLIAILAQL NPLFGPQLKN ETIWYLKYHW P

UniProtKB: V-type proton ATPase subunit e 1

Macromolecule #13: Ribonuclease kappa

• Macromolecule: Name: Ribonuclease kappa / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.43522 KDa

Sequence

String:

MGWLRPGPRP LCPPARASWA FSHRFPSPLA PRRSPTPFFM ASLLCCGPKL AACGIVLSAW GVIMLIMLGI FFNVHSAVLI EDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRLN KRKEYMVR

UniProtKB: Ribonuclease kappa

Macromolecule #14: V-type proton ATPase subunit S1

• Macromolecule: Name: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 52.06748 KDa

Sequence

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

UniProtKB: V-type proton ATPase subunit S1

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

• Macromolecule: Name: ATPase H(+)-transporting lysosomal accessory protein 2; type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 38.421098 KDa

Sequence

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

UniProtKB: Renin receptor

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

• Macromolecule: Name: V-type proton ATPase 16 kDa proteolipid subunit / type: protein_or_peptide / ID: 16 / Number of copies: 9 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.743655 KDa

Sequence

String:

MSESKSGPEY ASFFAVMGAS AAMVFSALGA AYGTAKSGTG IAAMSVMRPE QIMKSIIPVV MAGIIAIYGL VVAVLIANSL NDDISLYKS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

UniProtKB: V-type proton ATPase 16 kDa proteolipid subunit c

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

• Macromolecule: Name: V-type proton ATPase 21 kDa proteolipid subunit / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 21.418213 KDa

Sequence

String:

MTGLALLYSG VFVAFWACAL AVGVCYTIFD 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 c''

Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 20 / Number of copies: 1 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #21: 2-acetamido-2-deoxy-beta-D-glucopyranose

• Macromolecule: Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 21 / Number of copies: 6 / Formula: NAG
• Molecular weight: Theoretical: 221.208 Da

Chemical component information

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

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

• Macromolecule: Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate; type: ligand / ID: 22 / Number of copies: 9 / Formula: POV
• Molecular weight: Theoretical: 760.076 Da

Chemical component information

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

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination 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

Image processing

• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24984
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION