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- EMDB-77789: Arabidopsis thaliana V-type ATPase, State 1 bound to OXR5, Backbo... -

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Basic information

Entry
Database: EMDB / ID: EMD-77789
TitleArabidopsis thaliana V-type ATPase, State 1 bound to OXR5, Backbone model
Map data
Sample
  • Complex: Arabidopsis V-ATPase State 1
    • Protein or peptide: x 16 types
  • Ligand: x 2 types
KeywordsMembrane protein / protein complex / pH regulation / HYDROLASE
Function / homology
Function and homology information


trans-Golgi network transport vesicle membrane / proton-transporting V-type ATPase complex assembly / plant-type cell wall biogenesis / 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 ...trans-Golgi network transport vesicle membrane / proton-transporting V-type ATPase complex assembly / plant-type cell wall biogenesis / 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 / 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 / trans-Golgi network membrane / trans-Golgi network / chloroplast / cytoplasmic stress granule / cytosolic ribosome / actin filament binding / ATPase binding / protease binding / endosome / 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) / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / 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 ...: / Domain of unknown function (DUF7794) / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / 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 a1 / Uncharacterized protein At3g13410 / TLD-domain containing nucleolar protein / V-type proton ATPase subunit d1 / V-type proton ATPase subunit H ...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 a1 / Uncharacterized protein At3g13410 / TLD-domain containing nucleolar protein / 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: 4.3 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_77789.png

Downloads & links

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Map

FileDownload / File: emd_77789.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: 0.194
Minimum - Maximum-0.25775278 - 1.135585
Average (Standard dev.)0.016211974 (±0.04699262)
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: TLD-domain containing nucleolar protein OXR5
    • Protein or peptide: V-type proton ATPase subunit a1
    • 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
  • 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-#16
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: TLD-domain containing nucleolar protein OXR5

MacromoleculeName: TLD-domain containing nucleolar protein OXR5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 59.973324 KDa
SequenceString: MGASSSTDDK ESSEKREIES LAASTGALPL LKRSFSKLVD SQTNTVPFQS LKQSFGLSYD TITTEGEQKV SDLFPKLLEH LGSSLVDLF FVPDKEGLSW VEFASGYVKC CGRMSNSMSF NTLLRVYYVT AKNAGFSPKL EFESDEADCK INGSISVSEL L VFLWMCWT ...String:
MGASSSTDDK ESSEKREIES LAASTGALPL LKRSFSKLVD SQTNTVPFQS LKQSFGLSYD TITTEGEQKV SDLFPKLLEH LGSSLVDLF FVPDKEGLSW VEFASGYVKC CGRMSNSMSF NTLLRVYYVT AKNAGFSPKL EFESDEADCK INGSISVSEL L VFLWMCWT MSWDGRSSKA AEMKGCLFLP DISHLILSAV VSCTDSESGN SLDVWETDVS GLELELPIGK FLTWALMTVP CL TECLSHF CNSRLQNVTS AEDGSGPSKS TAVDDSASKT SENTLLTCGR AWAISLTSKS TISEEILSSC FPGNSGEPNE HLL YRSYYH GKGMNRLWSN VEGYHAPILV IISASCKVEH EATSSERKWV IGAILQQGFE NRDAFYGSSG NLFSISPVFH AFSS SGKEK NFAYSHLHPA GGVYDAHPKP VGIGFGGTLG NERIFIDEDF AKITVRHHAV DKTYQSGSLF PNQGYLPVEA LVLDI EAWG LGGNKAREIQ QKYQKREELF TNQRRKIDLK TFTNWEDSPE KMMMDMMGNP NAPRKEER

UniProtKB: TLD-domain containing nucleolar protein

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Macromolecule #2: V-type proton ATPase subunit a1

MacromoleculeName: V-type proton ATPase subunit a1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 93.512727 KDa
SequenceString: MEEFLDKLPQ MDLMRSEKMT LVQLIIPVES AHRSITYLGE LGLLQFRDLN ADKSPFQRTF ANQVKRCGEM SRKLRFFKDQ IDKAGLRCS PRLEIEPDIA LGDLERQLAD HEHEVLEMNS NSEKLRQTYN ELLEFKIVLE KASGFLVSSN THAIGEEIEL H ESTYSNNG ...String:
MEEFLDKLPQ MDLMRSEKMT LVQLIIPVES AHRSITYLGE LGLLQFRDLN ADKSPFQRTF ANQVKRCGEM SRKLRFFKDQ IDKAGLRCS PRLEIEPDIA LGDLERQLAD HEHEVLEMNS NSEKLRQTYN ELLEFKIVLE KASGFLVSSN THAIGEEIEL H ESTYSNNG FIETASLLEQ EMNPGHSNQS GLRFISGIIN KDKLLKFERM LFRATRGNML FNQTTSDEEI MDPSTSEMVE KV VFVVFFS GEQARTKILK ICEAFGANCY PVPEDTTKQR QLTREVLSRL SDLEATLDAG TRHRNNALNS VGYSLTNWIT TVR REKAVY DTLNMLNFDV TKKCLVGEGW CPTFAKTQIH EVLQRATFDS SSQVGVIFHV MQAVESPPTY FRTNKLTNAF QEII DAYGV ARYQEANPAV YSVVTYPFLF AVMFGDWGHG LCLLLGALYL LARERKLSTQ KLGSFMEMLF GGRYVILLMA LFSIY CGLI YNEFFSVPFH IFGGSAYKCR DTTCSDAYTV GLIKYRDPYP FGVDPSWRGS RTELPYLNSL KMKMSILLGI AQMNLG LIL SFFNARFFGS SLDIRYQFIP QMIFLNSLFG YLSLLIIIKW CTGSQADLYH VMIYMFLSPT EELGENELFW GQRPLQI VL LLLAFIAVPW MLFPKPFALR KIHMERFQGR TYGVLVSSEV DLDVEPDSAR GGGHHEEEFN FSEIFVHQLI HSIEFVLG S VSNTASYLRL WALSLAHSEL STVFYEKVLL LAWGYENILI RLIGVAVFAF ATAFILLMME TLSAFLHALR LHWVEFMGK FFNGDGYKFK PFSFALI

UniProtKB: V-type proton ATPase subunit a1

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Macromolecule #3: V-type proton ATPase subunit B1

MacromoleculeName: V-type proton ATPase subunit B1 / type: protein_or_peptide / ID: 3 / 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 #4: V-type proton ATPase subunit E1

MacromoleculeName: V-type proton ATPase subunit E1 / type: protein_or_peptide / ID: 4 / 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 #5: V-type proton ATPase subunit G1

MacromoleculeName: V-type proton ATPase subunit G1 / type: protein_or_peptide / ID: 5 / 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 #6: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 6 / 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 #7: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 7 / 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 #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: 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 #9: V-type proton ATPase subunit AP1 fragment

MacromoleculeName: V-type proton ATPase subunit AP1 fragment / type: protein_or_peptide / ID: 9 / 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 #10: V-type proton ATPase subunit c''1

MacromoleculeName: V-type proton ATPase subunit c''1 / type: protein_or_peptide / ID: 10 / 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 #11: V-type proton ATPase subunit d1

MacromoleculeName: V-type proton ATPase subunit d1 / type: protein_or_peptide / ID: 11 / 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 #12: V-type proton ATPase subunit e2

MacromoleculeName: V-type proton ATPase subunit e2 / type: protein_or_peptide / ID: 12 / 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 #13: V-type proton ATPase subunit c1

MacromoleculeName: V-type proton ATPase subunit c1 / type: protein_or_peptide / ID: 13 / 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 #14: V-type proton ATPase subunit AP2 fragment

MacromoleculeName: V-type proton ATPase subunit AP2 fragment / type: protein_or_peptide / ID: 14 / 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 #15: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 15 / 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 #16: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 16 / 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 #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: 4.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: cryoSPARC / Number images used: 5323
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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