[English] 日本語
Yorodumi
- EMDB-26827: Citrus V-ATPase State 2, Highest-Resolution Class -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26827
TitleCitrus V-ATPase State 2, Highest-Resolution Class
Map dataCitrus V-ATPase State 2, Highest-Resolution Class
Sample
  • Complex: Citrus V-ATPase
    • Protein or peptide: x 15 types
KeywordsV-ATPase / rotary ATPase / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / plant-type vacuole / vacuole / vacuolar acidification / vacuolar membrane ...proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / plant-type vacuole / vacuole / vacuolar acidification / vacuolar membrane / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / ATP metabolic process / endomembrane system / transmembrane transport / ATPase binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
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 / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H ...ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit G / V-type proton ATPase subunit F / V-type proton ATPase subunit e1 / V-type proton ATPase subunit D / Vacuolar proton pump subunit B / V-type proton ATPase subunit / V-type proton ATPase subunit C / V-type proton ATPase subunit c1 / Vacuolar membrane ATPase subunit c / V-type proton ATPase subunit E ...V-type proton ATPase subunit G / V-type proton ATPase subunit F / V-type proton ATPase subunit e1 / V-type proton ATPase subunit D / Vacuolar proton pump subunit B / V-type proton ATPase subunit / V-type proton ATPase subunit C / V-type proton ATPase subunit c1 / Vacuolar membrane ATPase subunit c / V-type proton ATPase subunit E / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit a
Similarity search - Component
Biological speciesCitrus limon (lemon)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTan YZ / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2022
Title: Structure of V-ATPase from citrus fruit.
Authors: Yong Zi Tan / Kristine A Keon / Rana Abdelaziz / Peter Imming / Waltraud Schulze / Karin Schumacher / John L Rubinstein /
Abstract: We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, ...We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme.
History
DepositionMay 3, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26827.png

Downloads & links

-
Map

FileDownload / File: emd_26827.map.gz / Format: CCP4 / Size: 15 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCitrus V-ATPase State 2, Highest-Resolution Class
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 200 pix.
= 323.4 Å		1.62 Å/pix.
x 140 pix.
= 226.38 Å		1.62 Å/pix.
x 140 pix.
= 226.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-0.46321112 - 5.6956472
Average (Standard dev.)0.12572032 (±0.2900597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140200
Spacing140140200
CellA: 226.38 Å / B: 226.38 Å / C: 323.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Citrus V-ATPase State 2, Highest-Resolution Class

Fileemd_26827_additional_1.map
AnnotationCitrus V-ATPase State 2, Highest-Resolution Class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Citrus V-ATPase State 2, Highest-Resolution Class

Fileemd_26827_half_map_1.map
AnnotationCitrus V-ATPase State 2, Highest-Resolution Class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Citrus V-ATPase State 2, Highest-Resolution Class

Fileemd_26827_half_map_2.map
AnnotationCitrus V-ATPase State 2, Highest-Resolution Class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Citrus V-ATPase

EntireName: Citrus V-ATPase
Components
  • Complex: Citrus V-ATPase
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B2
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: V-type proton ATPase subunit G
    • 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 C
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit a3
    • Protein or peptide: V-type proton ATPase subunit AP1 fragment
    • Protein or peptide: V-type proton ATPase subunit c"
    • Protein or peptide: V-type proton ATPase subunit d2
    • Protein or peptide: V-type proton ATPase subunit e1
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit AP2 fragment

+
Supramolecule #1: Citrus V-ATPase

SupramoleculeName: Citrus V-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Citrus limon (lemon)

+
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: Citrus limon (lemon)
Molecular weightTheoretical: 68.755219 KDa
SequenceString: MPSVYGARLT TFEDEEKESE YGYVRKVSGP VVIADGMNGA AMYELVRVGH DNLIGEIIRL EGDSATIQVY EETAGLMVND PVLRTHKPL SVELGPGILG NIFDGIQRPL KTIAIRSGDV YIPRGVSVPA LDKDTLWEFQ PKKIGEGDLL TGGDLYATVF E NSLMQHHV ...String:
MPSVYGARLT TFEDEEKESE YGYVRKVSGP VVIADGMNGA AMYELVRVGH DNLIGEIIRL EGDSATIQVY EETAGLMVND PVLRTHKPL SVELGPGILG NIFDGIQRPL KTIAIRSGDV YIPRGVSVPA LDKDTLWEFQ PKKIGEGDLL TGGDLYATVF E NSLMQHHV ALPPDAMGKV TYVAPAGQYS LKDTVLELEF QGVKKSFTML QAWPVRTPRP VSSKLAADTP LLTGQRVLDA LF PSVLGGT CAIPGAFGCG KTVISQALSK YSNSDTVVYV GCGERGNEMA EVLMDFPQLT MTLPDGREES VMKRTTLVAN TSN MPVAAR EASIYTGITI AEYFRDMGYN VSMMADSTSR WAEALREISG RLAEMPADSG YPAYLAARLA SFYERAGKVK CLGG PERTG SVTIVGAVSP PGGDFSDPVT SATLSIVQVF WGLDKKLAQR KHFPSVNWLI SYSKYSTALE SFYEQFDPDF INIRT KARE VLQREDDLNE IVQLVGKDAL AEGDKITLET AKLLREDYLA QNAFTPYDKF CPFYKSVWMM RNIIHFYNLA NQAVEK GAG MDGQKITYTL IKHRLGDLFY RLVSQKFEDP AEGEPALVAK FKKLHEDLTA GFRALEDETR

UniProtKB: V-type proton ATPase catalytic subunit A

+
Macromolecule #2: V-type proton ATPase subunit B2

MacromoleculeName: V-type proton ATPase subunit B2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 54.417594 KDa
SequenceString: MGVAQNNVDM EEGTLEVAME YRTVTGVAGP LVILDKVKGP KYYEIVNIRL GDGTMRRGQV LEVDGEKAVV QVFEGTSGID NKFTTVQFT GEVLKTPVSL DMLGRIFNGS GKPIDNGPPI LPEAYLDISG SSINPSERTY PEEMIQTGIS TIDVMNSIAR G QKIPLFSA ...String:
MGVAQNNVDM EEGTLEVAME YRTVTGVAGP LVILDKVKGP KYYEIVNIRL GDGTMRRGQV LEVDGEKAVV QVFEGTSGID NKFTTVQFT GEVLKTPVSL DMLGRIFNGS GKPIDNGPPI LPEAYLDISG SSINPSERTY PEEMIQTGIS TIDVMNSIAR G QKIPLFSA AGLPHNEIAA QICRQAGLVK RLEKTDNLLE DGEEDNFAIV FAAMGVNMET AQFFKRDFEE NGSMERVTLF LN LANDPTI ERIITPRIAL TTAEYLAYEC GKHVLVILTD MSSYADALRE VSAAREEVPG RRGYPGYMYT DLAQIYERAG RIE GRKGSI TQIPILTMPN DDITHPTPDL TGYITEGQIY IDRQLQNRQI YPPINVLPSL SRLMKSAIGE GMTRRDHSDV SNQL YANYA IGKDVQAMKA VVGEEALSSE DLLYLEFLDK FERKFVAQGA YDSRNIFQSL DLAWTLLRIF PRELLHRIPG KTLDQ YYSR DAAN

UniProtKB: Vacuolar proton pump subunit B

+
Macromolecule #3: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 26.331332 KDa
SequenceString: MNDADVSKQI QQMVRFIRQE AEEKANEISV SAEEEFNIEK LQLVEAEKKK IRQEYERKEK QVEIRKKIEY SMQLNASRIK VLQAQDDLV SNMMEAASKE VLNVSRDHNS YKKLLKGLIV QSLLRLKEPA VLLRCRKDDH HLVESVLESA KEEYAQKLQV H PPEIIVDH ...String:
MNDADVSKQI QQMVRFIRQE AEEKANEISV SAEEEFNIEK LQLVEAEKKK IRQEYERKEK QVEIRKKIEY SMQLNASRIK VLQAQDDLV SNMMEAASKE VLNVSRDHNS YKKLLKGLIV QSLLRLKEPA VLLRCRKDDH HLVESVLESA KEEYAQKLQV H PPEIIVDH HIYLPPGPGH HNAHGPSCSG GVVVASRDGK IVCENTLDAR LDVVFRKKLP EIRKQLVSQV AA

UniProtKB: V-type proton ATPase subunit E

+
Macromolecule #4: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 12.354938 KDa
SequenceString:
MASNRGHGGI QQLLAAEQEA QHIVAAARNA KMARLRQAKE EAEREIAEHR AQVEREFQRK LAESSGDSGA NVKRLEQETE VKIHHLNAG AEKIQYDVVQ MLLKHVTTVK N

UniProtKB: V-type proton ATPase subunit G

+
Macromolecule #5: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 29.235746 KDa
SequenceString: MAQNQRLTVV PTVTMLGVMK SRLVGATRGH ALLKKKSDAL TVQFRQILKN IVTTKESMGE VMKDSSFALI EAKYVAGENI KHIVLENVQ NASIKVRSRQ ENIAGVKIPK FEYFTDGETK NDLTGLARGG QQVQQCRAAY VKAIELLVEL ASLQTSFLTL D EAIKTTNR ...String:
MAQNQRLTVV PTVTMLGVMK SRLVGATRGH ALLKKKSDAL TVQFRQILKN IVTTKESMGE VMKDSSFALI EAKYVAGENI KHIVLENVQ NASIKVRSRQ ENIAGVKIPK FEYFTDGETK NDLTGLARGG QQVQQCRAAY VKAIELLVEL ASLQTSFLTL D EAIKTTNR RVNALENVVK PRLENTITYI KGELDELERE DFFRLKKIQG YKKREIERQL ASSKQFVEEQ FAEKVSLQKG IS IKSAQNL LSAGEKDEDI IF

UniProtKB: V-type proton ATPase subunit D

+
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: Citrus limon (lemon)
Molecular weightTheoretical: 14.301398 KDa
SequenceString:
MAGRAQIPTK SSALIAMIAD EDTVTGFLLA GVGNVDLRRK TNYLIVDSKT TVKAIEDAFK EFTTKEDIAI VLISQYVANM IRFLVDSYN KPIPAILEIP SKDHPYDPAH DSVLSRVKNL FSAESVASGR R

UniProtKB: V-type proton ATPase subunit F

+
Macromolecule #7: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 42.498875 KDa
SequenceString: MASRYWVVSL PVQNSAASVW NRLQEQISKH SFDTPLYRFN IPNLRVGTLD SLLALSDDLV KSNSFVESVS HKIRRQIEEL ERVSGIESS SLSVDGVPVD TYLTRFVWDE AKYPTMSPLR EIVDGIHTLV AKIEDDLKVR VAEYNNVRSQ LNAINRKQSG S LAVRDLSN ...String:
MASRYWVVSL PVQNSAASVW NRLQEQISKH SFDTPLYRFN IPNLRVGTLD SLLALSDDLV KSNSFVESVS HKIRRQIEEL ERVSGIESS SLSVDGVPVD TYLTRFVWDE AKYPTMSPLR EIVDGIHTLV AKIEDDLKVR VAEYNNVRSQ LNAINRKQSG S LAVRDLSN LVKPEDIITS EHLVTLLAVV PKYSQKDWLA SYETLTSYVV PRSSKLLYED NEYALYTVTL FGRVADNFRI AA REKGFQI RDFEYSSEAQ ESRNQELEKL VHDQESLRSS LLQWCYTSYG EVFSSWMHFC AVRVFAESIL RYGLPPSFLA CVL APSVKG EKKVRSILEE LCGNANSTFW KSEDDGGMMA GLGGDADSHP YVSFTINLV

UniProtKB: V-type proton ATPase subunit C

+
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: Citrus limon (lemon)
Molecular weightTheoretical: 51.609539 KDa
SequenceString: MDHAELTTEQ VLKRDIPWET YMTTKLISGT GLQLLRRYDN RSESHRAQLL DDDGPSYVRV FVSILRDIYK EETVEYVLAL IDEMLTANP KRARLFHDKS LASEDTYEPF LRLLWKGNWF IQEKSCKILA SIVSARPKPQ DRFFANGEAS NSKSKSTTID D VLKLLVEW ...String:
MDHAELTTEQ VLKRDIPWET YMTTKLISGT GLQLLRRYDN RSESHRAQLL DDDGPSYVRV FVSILRDIYK EETVEYVLAL IDEMLTANP KRARLFHDKS LASEDTYEPF LRLLWKGNWF IQEKSCKILA SIVSARPKPQ DRFFANGEAS NSKSKSTTID D VLKLLVEW LCAQLKKPSH PSRGVPVAIN CLAALLKEPM VRSSFVQADG VKLLTPLISP ASTQQSIQLL YETCLCVWLL SY YEPAVEY LATTRTLPRL IDVVKSSTKE KVVRVVVLIL RNLLPKGNFA AQMIDLGLPQ VVQSLKAQAW SDEDLLEGLN QLE EGLKDN IKRLSSFDKY KQEVLLGHLD WSPMHKDPLF WRDNITNFEE NDFQILRVLL TILDTSSDPR ALAVACFDLS QFIQ YHPAG RVIVTDLKAK ERVMKLMNHE NTEVTKSALL CIQRLFLGAK YASFLQA

+
Macromolecule #9: V-type proton ATPase subunit a3

MacromoleculeName: V-type proton ATPase subunit a3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 92.939797 KDa
SequenceString: MAELQSGGGG GCCPPMDLFR SEPMQLVQII IPIESAHLTV SYLGELGLLQ FKDLNSEKSP FQRTYAAQIK KCAEMARKLR FFKEQMLKA GILSSVKSTT RADNNTDDLE VKLGDLEAEL VEINANGDKL QRAHSELVEY KLVLQKAGEF FSSALTSAAA Q QREMESQQ ...String:
MAELQSGGGG GCCPPMDLFR SEPMQLVQII IPIESAHLTV SYLGELGLLQ FKDLNSEKSP FQRTYAAQIK KCAEMARKLR FFKEQMLKA GILSSVKSTT RADNNTDDLE VKLGDLEAEL VEINANGDKL QRAHSELVEY KLVLQKAGEF FSSALTSAAA Q QREMESQQ TGEMTIETPL LTDKEMSADP SKQIKLGFIA GLVPREKSMS FERMLFRATR GNVFLRQAVV DEPVVDPVSG EK MEKNVFV VFYSGERAKN KILKICDAFG ANRYPFNEEF DKQAQAISEV SGRLSELKTT LDAGLLHRGN LLQTIGDQFE QWN LLVKRE KSIYHTLNML SLDVTKKCLV GEGWSPVFAT KQIQDALERA AFDSNSQVGA IFQVLHTKES PPTYFRTNKF TSAF QEIVD AYGVAKYREA NPGVFTIVTF PFLFAVMFGD WGHGICLLLG TLVLIVREKK LASQKLDDIT DMTFGGRYVI LMMAL FSIY TGLIYNEFFS VPFEIFSHSA YACRDLSCSE ATTVGLIKVR DTYPFGVDPV WHGSRSELPF LNSLKMKMSI LLGVAQ MNL GIILSYFNAT FFRIGVNIWC QFIPQIIFLN SLFGYLSLLI ILKWITGSQA DLYHVMIYMF LSPTDELGDN QLFPGQK TA QLVLLLLAFV SVPWMLLPKP FILKMQHQDR HQGQSYEALQ STDESLQPDT NHDSHGHEEF EFSEVFVHQM IHTIEFVL G AVSNTASYLR LWALSLAHSE LSSVFYEKVL LLAWGYNNIL ILIVGIIVFI FATVGVLLVM ETLSAFLHAL RLHWVEFQN KFYEGDGYKF SPFSFALLDD EDE

UniProtKB: V-type proton ATPase subunit a

+
Macromolecule #10: V-type proton ATPase subunit AP1 fragment

MacromoleculeName: V-type proton ATPase subunit AP1 fragment / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 2.74137 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #11: V-type proton ATPase subunit c"

MacromoleculeName: V-type proton ATPase subunit c" / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 18.581932 KDa
SequenceString:
MSGSVMLGES SSWSRALVKI SPYTFSAIGI AVAIGVSVLG AAWGIYITGS SLIGAAIKAP RITSKNLISV IFCEAVAIYG VIVAIILQT KLESVPASQI YAPESLRAGY AIFASGIIVG FANLVCGLCV GIIGSSCALS DAQNSSLFVK ILVIEIFGSA L GLFGVIVG IIMSAQASWP AKPV

UniProtKB: Vacuolar membrane ATPase subunit c

+
Macromolecule #12: V-type proton ATPase subunit d2

MacromoleculeName: V-type proton ATPase subunit d2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 40.69341 KDa
SequenceString: MYGFEAMTFN IHGGYLEAIV RGYRAGLLTA ADYNNLCQCE TLDDIKMHLS ATEYGPYLQN EPSPLHTTTI VEKCTLKLVD EYKHMLCQA TEPLSTFLEY ITYGHMIDNV VLIVTGTLHE RDVQELLEKC HPLGMFDSIA TLAVAQNMRE LYRLVLVDTP L APYFSECI ...String:
MYGFEAMTFN IHGGYLEAIV RGYRAGLLTA ADYNNLCQCE TLDDIKMHLS ATEYGPYLQN EPSPLHTTTI VEKCTLKLVD EYKHMLCQA TEPLSTFLEY ITYGHMIDNV VLIVTGTLHE RDVQELLEKC HPLGMFDSIA TLAVAQNMRE LYRLVLVDTP L APYFSECI TSEDLDDMNI EIMRNTLYKA YLEDFYKFCQ KLGGATAEIM SDLLAFEADR RAVNITINSI GTELTRDDRR KL YSNFGLL YPYGHEELAV CEDIDQVRGV MEKYPPYQSI FSKLSYGESQ MLDKAFYEEE VKRLCLAFEQ QFHYGVFFAY MRL REQEIR NLMWISECVA QNQKSRVHDS VVFIF

UniProtKB: V-type proton ATPase subunit

+
Macromolecule #13: V-type proton ATPase subunit e1

MacromoleculeName: V-type proton ATPase subunit e1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 7.75746 KDa
SequenceString:
MGFLVTTLVF LVIGIIASLC TRICCNRGPS TNLLHLTLVI TATVSCWMMW AIVYLAQMKP LIVPILSEEE

UniProtKB: V-type proton ATPase subunit e1

+
Macromolecule #14: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 14 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
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

+
Macromolecule #15: V-type proton ATPase subunit AP2 fragment

MacromoleculeName: V-type proton ATPase subunit AP2 fragment / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Citrus limon (lemon)
Molecular weightTheoretical: 2.060531 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.414211 µm / Nominal defocus min: 0.677558 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104874
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more