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- EMDB-77786: Arabidopsis thaliana V-type ATPase, State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-77786
TitleArabidopsis thaliana V-type ATPase, State 1
Map data
Sample
  • Complex: Arabidopsis V-ATPase State 1
    • Protein or peptide: x 15 types
  • Ligand: x 3 types
KeywordsMembrane protein / protein complex / pH regulation / HYDROLASE
Function / homology
Function and homology information


regulation of auxin polar transport / zinc ion sequestering activity / plant-type cell wall biogenesis / diphosphate hydrolysis-driven proton transmembrane transporter activity / proton-transporting two-sector ATPase complex / unidimensional cell growth / glucose mediated signaling pathway / plant-type vacuole membrane / proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain ...regulation of auxin polar transport / zinc ion sequestering activity / plant-type cell wall biogenesis / diphosphate hydrolysis-driven proton transmembrane transporter activity / proton-transporting two-sector ATPase complex / unidimensional cell growth / glucose mediated signaling pathway / plant-type vacuole membrane / proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain / lysosomal lumen acidification / pollen development / proton-transporting V-type ATPase, V0 domain / plant-type cell wall / embryo development ending in seed dormancy / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / negative regulation of actin filament depolymerization / vacuolar proton-transporting V-type ATPase complex / plasmodesma / plant-type vacuole / chloroplast envelope / vacuolar acidification / actin filament capping / vacuole / vacuolar membrane / proton motive force-driven ATP synthesis / Golgi organization / proton-transporting ATPase activity, rotational mechanism / actin filament bundle assembly / H+-transporting two-sector ATPase / ATP metabolic process / response to cold / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / chloroplast / cytoplasmic stress granule / cytosolic ribosome / actin filament binding / ATPase binding / protease binding / structural constituent of ribosome / Golgi membrane / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular region / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Domain of unknown function (DUF7794) / 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 ...: / Domain of unknown function (DUF7794) / 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 / 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 catalytic subunit A / V-type proton ATPase subunit G1 / V-type proton ATPase subunit c1 / V-type proton ATPase subunit B1 / V-type proton ATPase subunit E1 / V-type proton ATPase subunit a3 / Uncharacterized protein At3g13410 / V-type proton ATPase subunit d1 / V-type proton ATPase subunit H / V-type proton ATPase subunit C ...V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit G1 / V-type proton ATPase subunit c1 / V-type proton ATPase subunit B1 / V-type proton ATPase subunit E1 / V-type proton ATPase subunit a3 / Uncharacterized protein At3g13410 / V-type proton ATPase subunit d1 / V-type proton ATPase subunit H / V-type proton ATPase subunit C / V-type proton ATPase subunit e2 / V-type proton ATPase subunit c''1 / V-type proton ATPase subunit D / V-type proton ATPase subunit F / AT3g24160/MUJ8_16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKhamina M / Rubinstein JL
Funding support Canada, Germany, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT195707 Canada
German Research Foundation (DFG)CRC1101 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana V-type ATPase
Authors: Khamina M / Wunsch N / Lupanga U / Fink F / Wang H / Schulze WX / Schumacher K / Rubinstein JL
History
DepositionJun 26, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77786.png

Downloads & links

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Map

FileDownload / File: emd_77786.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.10680464 - 1.8364428
Average (Standard dev.)0.020142537 (±0.051287763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 476.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Arabidopsis V-ATPase State 1

EntireName: Arabidopsis V-ATPase State 1
Components
  • Complex: Arabidopsis V-ATPase State 1
    • Protein or peptide: V-type proton ATPase subunit B1
    • Protein or peptide: V-type proton ATPase subunit E1
    • Protein or peptide: V-type proton ATPase subunit G1
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit AP1 fragment
    • Protein or peptide: V-type proton ATPase subunit c''1
    • Protein or peptide: V-type proton ATPase subunit d1
    • Protein or peptide: V-type proton ATPase subunit e2
    • Protein or peptide: V-type proton ATPase subunit c1
    • Protein or peptide: V-type proton ATPase subunit AP2 fragment
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit C
    • Protein or peptide: V-type proton ATPase subunit a3
  • Ligand: PALMITIC ACID
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Arabidopsis V-ATPase State 1

SupramoleculeName: Arabidopsis V-ATPase State 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: V-type proton ATPase subunit B1

MacromoleculeName: V-type proton ATPase subunit B1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 54.164352 KDa
SequenceString: MGTNDLDIEE GTLEIGMEYR TVSGVAGPLV ILDKVKGPKY QEIVNIRLGD GSTRRGQVLE VDGEKAVVQV FEGTSGIDNK FTTVQFTGE VLKTPVSLDM LGRIFNGSGK PIDNGPPILP EAYLDISGSS INPSERTYPE EMIQTGISTI DVMNSIARGQ K IPLFSAAG ...String:
MGTNDLDIEE GTLEIGMEYR TVSGVAGPLV ILDKVKGPKY QEIVNIRLGD GSTRRGQVLE VDGEKAVVQV FEGTSGIDNK FTTVQFTGE VLKTPVSLDM LGRIFNGSGK PIDNGPPILP EAYLDISGSS INPSERTYPE EMIQTGISTI DVMNSIARGQ K IPLFSAAG LPHNEIAAQI CRQAGLVKRL EKTVDLLEDH GEDNFAIVFA AMGVNMETAQ FFKRDFEENG SMERVTLFLN LA NDPTIER IITPRIALTT AEYLAYECGK HVLVILTDMS SYADALREVS AAREEVPGRR GYPGYMYTDL ATIYERAGRI EGR KGSITQ IPILTMPNDD ITHPTPDLTG YITEGQIYID RQLHNRQIYP PINVLPSLSR LMKSAIGEGM TRKDHSDVSN QLYA NYAIG KDVQAMKAVV GEEALSSEDL LYLEFLDKFE RKFVMQGAYD TRNIFQSLDL AWTLLRIFPR ELLHRIPAKT LDQFY SRDS TS

UniProtKB: V-type proton ATPase subunit B1

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Macromolecule #2: V-type proton ATPase subunit E1

MacromoleculeName: V-type proton ATPase subunit E1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.101053 KDa
SequenceString: MNDGDVSRQI QQMVRFIRQE AEEKANEISV SAEEEFNIEK LQLVEAEKKK IRQDYEKKEK QADVRKKIDY SMQLNASRIK VLQAQDDIV NAMKDQAAKD LLNVSRDEYA YKQLLKDLIV QCLLRLKEPS VLLRCREEDL GLVEAVLDDA KEEYAGKAKV H APEVAVDT ...String:
MNDGDVSRQI QQMVRFIRQE AEEKANEISV SAEEEFNIEK LQLVEAEKKK IRQDYEKKEK QADVRKKIDY SMQLNASRIK VLQAQDDIV NAMKDQAAKD LLNVSRDEYA YKQLLKDLIV QCLLRLKEPS VLLRCREEDL GLVEAVLDDA KEEYAGKAKV H APEVAVDT KIFLPPPPKS NDPHGLHCSG GVVLASRDGK IVCENTLDAR LDVAFRMKLP VIRKSLFGQV TA

UniProtKB: V-type proton ATPase subunit E1

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Macromolecule #3: V-type proton ATPase subunit G1

MacromoleculeName: V-type proton ATPase subunit G1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.416915 KDa
SequenceString:
MESNRGQGSI QQLLAAEVEA QHIVNAARTA KMARLKQAKE EAEKEIAEYK AQTEQDFQRK LEETSGDSGA NVKRLEQETD TKIEQLKNE ASRISKDVVE MLLKHVTTVK N

UniProtKB: V-type proton ATPase subunit G1

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 29.104756 KDa
SequenceString: MAGQNARLNV VPTVTMLGVM KARLVGATRG HALLKKKSDA LTVQFRALLK KIVTAKESMG DMMKTSSFAL TEVKYVAGDN VKHVVLENV KEATLKVRSR TENIAGVKLP KFDHFSEGET KNDLTGLARG GQQVRACRVA YVKAIEVLVE LASLQTSFLT L DEAIKTTN ...String:
MAGQNARLNV VPTVTMLGVM KARLVGATRG HALLKKKSDA LTVQFRALLK KIVTAKESMG DMMKTSSFAL TEVKYVAGDN VKHVVLENV KEATLKVRSR TENIAGVKLP KFDHFSEGET KNDLTGLARG GQQVRACRVA YVKAIEVLVE LASLQTSFLT L DEAIKTTN RRVNALENVV KPKLENTISY IKGELDELER EDFFRLKKIQ GYKRREVERQ AANAKEFAEE MVLEDISMQR GI SINAARN FLVGGAEKDS DIIF

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #5: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.276354 KDa
SequenceString:
MAGRATIPAR NSALIAMIAD EDTVVGFLMA GVGNVDIRRK TNYLIVDSKT TVRQIEDAFK EFSARDDIAI ILLSQYIANM IRFLVDSYN KPVPAILEIP SKDHPYDPAH DSVLSRVKYL FSAESVSQR

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #6: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.346262 KDa
SequenceString: MDQAELSIEQ VLKRDIPWET YMNTKLVSAK GLQLLRRYDK KPESARAQLL DEDGPAYVHL FVSILRDIFK EETVEYVLAL IYEMLSANP TRARLFHDES LANEDTYEPF LRLLWKGNWF IQEKSCKILA WIISARPKAG NAVIGNGIDD VLKGLVEWLC A QLKQPSHP ...String:
MDQAELSIEQ VLKRDIPWET YMNTKLVSAK GLQLLRRYDK KPESARAQLL DEDGPAYVHL FVSILRDIFK EETVEYVLAL IYEMLSANP TRARLFHDES LANEDTYEPF LRLLWKGNWF IQEKSCKILA WIISARPKAG NAVIGNGIDD VLKGLVEWLC A QLKQPSHP TRGVPIAISC LSSLLKEPVV RSSFVQADGV KLLVPLISPA STQQSIQLLY ETCLCIWLLS YYEPAIEYLA TS RTMQRLT EVVKHSTKEK VVRVVILTFR NLLPKGTFGA QMVDLGLPHI IHSLKTQAWS DEDLLDALNQ LEEGLKDKIK KLS SFDKYK QEVLLGHLDW NPMHKETNFW RENVTCFEEN DFQILRVLLT ILDTSSDPRS LAVACFDISQ FIQYHAAGRV IVAD LKAKE RVMKLINHEN AEVTKNAILC IQRLLLGAKY ASFLQA

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #7: V-type proton ATPase subunit AP1 fragment

MacromoleculeName: V-type proton ATPase subunit AP1 fragment / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 35.015453 KDa
SequenceString: MKKIQIGAVA LLVFLSVASL FEIGLASPNT VPAFLWSPHL QSANGELDEA VNYQVMSAKD LVGSVFTQGG WSNFLCSEKK LEQPVDVAL VFIGRELLSS DVSSKRNSDP ALVNTLNNLF TASNFSLAFP YIAAPEEERM ENLLLSGLKE ACPNNVGVSN I VFSDSCFV ...String:
MKKIQIGAVA LLVFLSVASL FEIGLASPNT VPAFLWSPHL QSANGELDEA VNYQVMSAKD LVGSVFTQGG WSNFLCSEKK LEQPVDVAL VFIGRELLSS DVSSKRNSDP ALVNTLNNLF TASNFSLAFP YIAAPEEERM ENLLLSGLKE ACPNNVGVSN I VFSDSCFV EDGTIQKLSD LQSFKDHLLA RRETRKEGET DLVVLCSEGS ESNSQAGQSH SERESFLELV SSVEQSGSKY TA LYVSDPY WYTSYKTLQR FLAETAKGNS TPEIATGCDE LCKFKSSLLE GILVGIVFLL ILISGLCCMA GIDTPTRFET PQD S

UniProtKB: Uncharacterized protein At3g13410

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Macromolecule #8: V-type proton ATPase subunit c''1

MacromoleculeName: V-type proton ATPase subunit c''1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 18.383625 KDa
SequenceString:
MSGVVALGHA SSWGAALVRI SPYTFSAIGI AISIGVSVLG AAWGIYITGS SLIGAAIEAP RITSKNLISV IFCEAVAIYG VIVAIILQT KLESVPSSKM YDAESLRAGY AIFASGIIVG FANLVCGLCV GIIGSSCALS DAQNSTLFVK ILVIEIFGSA L GLFGVIVG IIMSAQATWP TK

UniProtKB: V-type proton ATPase subunit c''1

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Macromolecule #9: V-type proton ATPase subunit d1

MacromoleculeName: V-type proton ATPase subunit d1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 40.835688 KDa
SequenceString: MYGFEALTFN IHGGYLEAIV RGHRAGLLTT ADYNNLCQCE NLDDIKMHLS ATKYGSYLQN EPSPLHTTTI VEKCTLKLVD DYKHMLCQA TEPMSTFLEY IRYGHMIDNV VLIVTGTLHE RDVQELIEKC HPLGMFDSIA TLAVAQNMRE LYRLVLVDTP L APYFSECL ...String:
MYGFEALTFN IHGGYLEAIV RGHRAGLLTT ADYNNLCQCE NLDDIKMHLS ATKYGSYLQN EPSPLHTTTI VEKCTLKLVD DYKHMLCQA TEPMSTFLEY IRYGHMIDNV VLIVTGTLHE RDVQELIEKC HPLGMFDSIA TLAVAQNMRE LYRLVLVDTP L APYFSECL TSEDLDDMNI EIMRNTLYKA YLEDFYKFCQ KLGGATAEIM SDLLAFEADR RAVNITINSI GTELTREDRK KL YSNFGLL YPYGHEELAI CEDIDQVRGV MEKYPPYQAI FSKMSYGESQ MLDKAFYEEE VRRLCLAFEQ QFHYAVFFAY MRL REQEIR NLMWISECVA QNQKSRIHDS VVYMF

UniProtKB: V-type proton ATPase subunit d1

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Macromolecule #10: V-type proton ATPase subunit e2

MacromoleculeName: V-type proton ATPase subunit e2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.688377 KDa
SequenceString:
MAFVVTSLIF AVVGIIASIC TRICFNKGPS TNLLHLTLVI TATVCCWMMW AIVYIAQMNP LIVPILSEVE

UniProtKB: V-type proton ATPase subunit e2

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Macromolecule #11: V-type proton ATPase subunit c1

MacromoleculeName: V-type proton ATPase subunit c1 / type: protein_or_peptide / ID: 11 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.581588 KDa
SequenceString:
MSTFSGDETA PFFGFLGAAA ALVFSCMGAA YGTAKSGVGV ASMGVMRPEL VMKSIVPVVM AGVLGIYGLI IAVIISTGIN PKAKSYYLF DGYAHLSSGL ACGLAGLSAG MAIGIVGDAG VRANAQQPKL FVGMILILIF AEALALYGLI VGIILSSRAG Q SRAE

UniProtKB: V-type proton ATPase subunit c1

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Macromolecule #12: V-type proton ATPase subunit AP2 fragment

MacromoleculeName: V-type proton ATPase subunit AP2 fragment / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.164426 KDa
SequenceString: MKAFYVFVVA LLLTLNYRGE ASGSVFFIDG SNNQYLRPRS SSEALPMSPV EISAAVSALL GFAPSATLTA DGSSKLNKIL KPNPFERPR AAFVLEIAGA DDMLLETSPS HSFLGNAIRS SIKSDSYKAD TELPDNEVVV VSVNEPSSDV TDKDINDFAS W LGGSYVAG ...String:
MKAFYVFVVA LLLTLNYRGE ASGSVFFIDG SNNQYLRPRS SSEALPMSPV EISAAVSALL GFAPSATLTA DGSSKLNKIL KPNPFERPR AAFVLEIAGA DDMLLETSPS HSFLGNAIRS SIKSDSYKAD TELPDNEVVV VSVNEPSSDV TDKDINDFAS W LGGSYVAG AEPSSGLLSI PLAGGANVEF NLEKEAERKF ALNLLGLYQN IRQAVSVYDD LSHGIDRTAE LTVGRFGGID AL AQEYGQG MAKQGMDVLL STLSKLFNLL ETSHKGQIVG VIVLDERVNQ ESENLLNFGS SRSSARSMVE VEGIPSAAII AEV ILVRLT LAWLTGIILL IATILGVYFL MNMPLTKDTL LYSNVKLD

UniProtKB: AT3g24160/MUJ8_16

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Macromolecule #13: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 13 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 68.884234 KDa
SequenceString: MPAFYGGKLT TFEDDEKESE YGYVRKVSGP VVVADGMAGA AMYELVRVGH DNLIGEIIRL EGDSATIQVY EETAGLTVND PVLRTHKPL SVELGPGILG NIFDGIQRPL KTIARISGDV YIPRGVSVPA LDKDCLWEFQ PNKFVEGDTI TGGDLYATVF E NTLMNHLV ...String:
MPAFYGGKLT TFEDDEKESE YGYVRKVSGP VVVADGMAGA AMYELVRVGH DNLIGEIIRL EGDSATIQVY EETAGLTVND PVLRTHKPL SVELGPGILG NIFDGIQRPL KTIARISGDV YIPRGVSVPA LDKDCLWEFQ PNKFVEGDTI TGGDLYATVF E NTLMNHLV ALPPDAMGKI TYIAPAGQYS LKDTVIELEF QGIKKSYTML QSWPVRTPRP VASKLAADTP LLTGQRVLDA LF PSVLGGT CAIPGAFGCG KTVISQALSK YSNSDAVVYV GCGERGNEMA EVLMDFPQLT MTLPDGREES VMKRTTLVAN TSN MPVAAR EASIYTGITI AEYFRDMGYN VSMMADSTSR WAEALREISG RLAEMPADSG YPAYLAARLA SFYERAGKVK CLGG PERNG SVTIVGAVSP PGGDFSDPVT SATLSIVQVF WGLDKKLAQR KHFPSVNWLI SYSKYSTALE SFYEKFDPDF INIRT KARE VLQREDDLNE IVQLVGKDAL AEGDKITLET AKLLREDYLA QNAFTPYDKF CPFYKSVWMM RNIIHFYNLA NQAVER AAG MDGQKITYTL IKHRLGDLFY RLVSQKFEDP AEGEDTLVEK FKKLYDDLNA GFRALEDETR

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #14: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 42.667199 KDa
SequenceString: MTSRYWVVSL PVKDSASSLW NRLQEQISKH SFDTPVYRFN IPNLRVGTLD SLLALGDDLL KSNSFVEGVS QKIRRQIEEL ERISGVESN ALTVDGVPVD SYLTRFVWDE AKYPTMSPLK EVVDNIQSQV AKIEDDLKVR VAEYNNIRGQ LNAINRKQSG S LAVRDLSN ...String:
MTSRYWVVSL PVKDSASSLW NRLQEQISKH SFDTPVYRFN IPNLRVGTLD SLLALGDDLL KSNSFVEGVS QKIRRQIEEL ERISGVESN ALTVDGVPVD SYLTRFVWDE AKYPTMSPLK EVVDNIQSQV AKIEDDLKVR VAEYNNIRGQ LNAINRKQSG S LAVRDLSN LVKPEDIVES EHLVTLLAVV PKYSQKDWLA CYETLTDYVV PRSSKKLFED NEYALYTVTL FTRVADNFRI AA REKGFQV RDFEQSVEAQ ETRKQELAKL VQDQESLRSS LLQWCYTSYG EVFSSWMHFC AVRTFAESIM RYGLPPAFLA CVL SPAVKS EKKVRSILER LCDSTNSLYW KSEEDAGAMA GLAGDSETHP YVSFTINLA

UniProtKB: V-type proton ATPase subunit C

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Macromolecule #15: V-type proton ATPase subunit a3

MacromoleculeName: V-type proton ATPase subunit a3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 92.928086 KDa
SequenceString: MAESGGGGGC CPPMDLMRSE TMQLVQLIVP MESAHLTVSY LGDLGLVQFK DLNSEKSPFQ RTYAAQIKRC GEMARKIRFF RDQMSKAGV PAKEMQGKEN DIDLDDVEVK LGELEAELVE INANNDKLQR SYNELMEYKL VLQKAGEFFS SAHRSAADQQ R ETESQQAG ...String:
MAESGGGGGC CPPMDLMRSE TMQLVQLIVP MESAHLTVSY LGDLGLVQFK DLNSEKSPFQ RTYAAQIKRC GEMARKIRFF RDQMSKAGV PAKEMQGKEN DIDLDDVEVK LGELEAELVE INANNDKLQR SYNELMEYKL VLQKAGEFFS SAHRSAADQQ R ETESQQAG EDLLESPLLQ EEKSIDSTKQ VKLGFLTGLV PREKSMVFER ILFRATRGNI FIRQTVIEEP VIDPNSGEKA EK NVFVVFY SGERAKSKIL KICEAFGANR YPFSEDLGRQ AQMITEVSGR LSELKTTIDA GLGQRNILLQ TIGDKFELWN LKV RKEKAI YHTLNMLSLD VTKKCLVAEG WSPVFASREI QDALQRAAVD SNSQVGSIFQ VLRTKESPPT YFRTNKFTSA IQEI VDAYG VAKYQEANPG VFTIVTFPFL FAVMFGDWGH GICILLATMY LILKEKKLAS QKLGDIMEMA FGGRYVILMM SLFSI YTGL IYNEFFSIPF PLFAPSAYDC RDVSCSEATT IGLIKVRDTY PFGLDPVWHG SRSELPFLNS LKMKMSILLG VSQMNL GII MSYFNARFFK SSVNIWFQFI PQMIFLNSLF GYLSVLIIIK WCTGSQADLY HVMIYMFLSP MDELGENQLF PHQKTLQ LV LLFLALVSVP CMLLPKPFIL KKQHEARHQG QAYAPLDETD ESLHVETNGG GSHGHEEFEF SEIFVHQLIH TIEFVLGA V SNTASYLRLW ALSLAHSELS SVFYEKVLLL AWGYNNPLIL IVGVLVFIFA TVGVLLVMET LSAFLHALRL HWVEFQNKF YEGDGYKFAP FTFIFTANED E

UniProtKB: V-type proton ATPase subunit a3

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Macromolecule #16: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 16 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #17: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 17 / 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 #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 3.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 7681 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 190490
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54020
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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