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- EMDB-22121: Cryo-EM structure of V-ATPase from bovine brain, state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-22121
TitleCryo-EM structure of V-ATPase from bovine brain, state 1
Map dataStructure of V-ATPase from bovine brain, state 1
Sample
  • Complex: Cryo-EM structure of V-ATPase complex from bovine brain, state 1
    • Protein or peptide: x 16 types
  • Ligand: x 5 types
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 / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / protein localization to cilium / transmembrane transporter complex / dendritic spine membrane / regulation of cellular pH / Neutrophil degranulation / microtubule organizing center / autophagosome membrane / microvillus / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / RNA endonuclease activity / transport vesicle / ruffle / proton-transporting ATPase activity, rotational mechanism / receptor-mediated endocytosis / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / cilium / transmembrane transport / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / presynapse / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / lysosome / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
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, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / 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
V-type proton ATPase subunit D / V-type proton ATPase subunit a / V-type proton ATPase subunit H / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit D / V-type proton ATPase subunit S1 ...V-type proton ATPase subunit D / V-type proton ATPase subunit a / V-type proton ATPase subunit H / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit D / V-type proton ATPase subunit S1 / V-type proton ATPase subunit d 1 / Renin receptor / V-type proton ATPase subunit G 2 / V-type proton ATPase subunit F / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit e 2 / V-type proton ATPase 21 kDa proteolipid subunit c'' / Ribonuclease kappa
Similarity search - Component
Biological speciesBos taurus (cattle) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWang R / Li X
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures of intact V-ATPase from bovine brain.
Authors: Rong Wang / Tao Long / Abdirahman Hassan / Jin Wang / Yingyuan Sun / Xiao-Song Xie / Xiaochun Li /
Abstract: The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been ...The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission.
History
DepositionJun 7, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xbw
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22121.png

Downloads & links

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Map

FileDownload / File: emd_22121.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of V-ATPase from bovine brain, state 1
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 4 / Movie #1: 4.5
Minimum - Maximum-17.506342 - 31.87527
Average (Standard dev.)0.01497498 (±1.1287838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 424.83002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z424.830424.830424.830
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-17.50631.8750.015

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of V-ATPase complex from bovine brain, state 1

EntireName: Cryo-EM structure of V-ATPase complex from bovine brain, state 1
Components
  • Complex: Cryo-EM structure of V-ATPase complex from bovine brain, state 1
    • 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 C 1
    • 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: 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
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: Renin receptor
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit
    • Protein or peptide: Ribonuclease kappa
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: OLEIC ACID

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Supramolecule #1: Cryo-EM structure of V-ATPase complex from bovine brain, state 1

SupramoleculeName: Cryo-EM structure of V-ATPase complex from bovine brain, state 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
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: Bovine (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

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Macromolecule #2: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bovine (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

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Macromolecule #3: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 44.042566 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI 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 TMKKLREVLY ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

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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: Bovine (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

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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: Bovine (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

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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: Bovine (cattle)
Molecular weightTheoretical: 13.417275 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA RGMFTAEDLR

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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: Bovine (cattle)
Molecular weightTheoretical: 13.588344 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVDQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLAQL LGMVCDVRPQ VHPNYRIAA

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Macromolecule #8: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 54.155875 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISSEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTLVDD TLQENHQRVS IFFDYAKRSK NTAWSYFLPM LNRQDLFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISSEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTLVDD TLQENHQRVS IFFDYAKRSK NTAWSYFLPM LNRQDLFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLSSQSSQ YVQCVAGCLQ LMLRVNEYRF AWVEADGVNC IMGVLSNKCG FQLQYQMIFS VWLLAFSPQM CE HLRRYNI IPVLSDILQE SVKEKVTRII LAAFRNFLEK SVERETRQEY ALAMIQCKVL KQLENLEQQK YDDEDISEDI KFL LEKLGE SVQDLSSFDE YSSELKSGRL EWSPVHKSEK FWRENAARLN EKNYELLKIL TKLLEVSDDP QVLAVAAHDV GEYV RHYPR GKRVIEQLGG KQLVMNHMHH EDQQVRYNAL LAVQKLMVHN WEYLGKQLQS EQPQTAAARS

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Macromolecule #9: V-type proton ATPase subunit a

MacromoleculeName: V-type proton ATPase subunit a / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 96.431398 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPSE M GRGTPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPSE M GRGTPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTYGFQN IVDAYGIGTY REINPAPYTI ITFP FLFAV MFGDLGHGIL MTLFAVWMVL RESRILSQKN ENEMFSTIFS GRYIILLMGV FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FDIYNWTEET LRGNPVLQLN PAVTGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMLFGVS LSLFNH TYF KKPLNIYFGF IPEIIFMTSL FGYLVILIFY KWTAYNAKTS EKAPSLLIHF INMFLFSYGD SGNSMLYSGQ KGIQCFL VV VALLCVPWML LFKPLVLRRQ YLRRKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLKVKSLA GGLALFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYSGTG FKFLPFSFEH IREGKFDD

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Macromolecule #10: V-type proton ATPase 21 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
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

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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: Bovine (cattle)
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 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 9.188992 KDa
SequenceString:
MTAHSFALPV VIFTTFWGLI GIAGPWFVPK GPNRGVIITM LVATAVCCYL FWLIAILAQL NPLFGPQLKN ETIWYVRFLW E

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Macromolecule #13: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 51.818754 KDa
SequenceString: MMAATAAAQV RAGTRWAPAL CRMPWLPLML VAAAAATSEQ QVPLVLWSSD RGLWAPAADT HEGHITSDMQ LSTYLDPALE LGPRNVLLF LQDKLSIEDF TAYGGVFGNK QDSAFSNLEN ALDLAPSSLV LPAVDWYAIS TLTTYLQEKL GASPLHVDLA T LQELKLNA ...String:
MMAATAAAQV RAGTRWAPAL CRMPWLPLML VAAAAATSEQ QVPLVLWSSD RGLWAPAADT HEGHITSDMQ LSTYLDPALE LGPRNVLLF LQDKLSIEDF TAYGGVFGNK QDSAFSNLEN ALDLAPSSLV LPAVDWYAIS TLTTYLQEKL GASPLHVDLA T LQELKLNA SIPALLLIRL PYTASSGLMA PKEVLMGNDE VIGQVLSTLK SEDIPYTAAL TAVRPSRVAR DVAMVTGGLG RQ LLQRTVV PPTMNVPVSY NDSYDTRILF WAQNFSVAYG EHWEDLTSRT FGVQDLNLTG SFWNDTVARL VLTYDSLFGT MVT FKFILA NSYYSVSARH WFTLENLEIH SNGSVAYFNA SQVTGPSIYS FHCEHVSSEN EDGNLLVPDT QPSLWQMTFR DFQI QAFNV TDKKFSYASD CAGFFSPGIW MGLLTSLFML FIFTYGLHMI LSLKTMDRFD DHKGPTITLT QIV

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Macromolecule #14: Renin receptor

MacromoleculeName: Renin receptor / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 39.529266 KDa
SequenceString: MAVLVVFLSF LVADVFGNEF SILRSPGSVV FRNGNWPIPG ERIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATVMVM VKGVDKLAL PPGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLTS ...String:
MAVLVVFLSF LVADVFGNEF SILRSPGSVV FRNGNWPIPG ERIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATVMVM VKGVDKLAL PPGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLTS LPLNSLSRNN EVDLLFLSEL QVLRDISSLL SRHKHLAKDH SPDLYSLELA GLDEIGKHYG EDSEQFRDAS KI LIDALQK FADDMYNLYG GNAVVELVTV RSFDTSLVRK TRNILETKQV KDPSTTYNLA YKYNFEYPVV FNLVLWIMIG LAL TLIVTC YNIWNMDPGY DSIIYRMTNQ KIRMD

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Macromolecule #15: V-type proton ATPase 16 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit / type: protein_or_peptide / ID: 15 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 15.727726 KDa
SequenceString:
MSEAKNGPEY ASFFAVMGAS AAMVFSALGA AYGTAKSGTG IAAMSVMRPE MIMKSIIPVV MAGIIAIYGL VVAVLIANSL NDGISLYRS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

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Macromolecule #16: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Bovine (cattle)
Molecular weightTheoretical: 11.030029 KDa
SequenceString:
MASLLCCGPK LAACGIVLSA WGVIMLIMLG IFFNVHSAVL IEDVPFTEKD FENGPQNIYN LYEQVSYNCF IAASLYLLLG GFSFCQVRL NKRKEYMVR

+
Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
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 / Adenosine diphosphate

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Macromolecule #19: (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: 19 / 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 / POPC

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Macromolecule #20: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 20 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

+
Macromolecule #21: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 21 / Number of copies: 1 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID / Oleic acid

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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
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

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84345

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