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- EMDB-21849: Human V-ATPase in state 3 with SidK and ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-21849
TitleHuman V-ATPase in state 3 with SidK and ADP
Map dataHuman V-ATPase in state 3 (composite map)
Sample
  • Complex: Human V-ATPase with SidK and ADP
    • Protein or peptide: x 17 types
  • Ligand: x 2 types
Keywordspump / MEMBRANE PROTEIN
Function / homology
Function and homology information


Blockage of phagosome acidification / proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / symbiont-mediated suppression of host phagosome acidification / plasma membrane proton-transporting V-type ATPase complex / Nef Mediated CD8 Down-regulation / eye pigmentation / central nervous system maturation ...Blockage of phagosome acidification / proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / symbiont-mediated suppression of host phagosome acidification / plasma membrane proton-transporting V-type ATPase complex / Nef Mediated CD8 Down-regulation / eye pigmentation / central nervous system maturation / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / Golgi lumen acidification / synaptic vesicle lumen acidification / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Transferrin endocytosis and recycling / cellular response to increased oxygen levels / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / head morphogenesis / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / osteoclast development / Nef Mediated CD4 Down-regulation / ROS and RNS production in phagocytes / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / azurophil granule membrane / microvillus / proton transmembrane transporter activity / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / tertiary granule membrane / ficolin-1-rich granule membrane / proton-transporting ATPase activity, rotational mechanism / cilium assembly / RHOA GTPase cycle / positive regulation of Wnt signaling pathway / regulation of macroautophagy / transporter activator activity / H+-transporting two-sector ATPase / ATP metabolic process / specific granule membrane / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / Insulin receptor recycling / enzyme regulator activity / ruffle / receptor-mediated endocytosis of virus by host cell / proton-transporting ATP synthase activity, rotational mechanism / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / secretory granule / secretory granule membrane / small GTPase binding / transmembrane transport / phagocytic vesicle membrane / endocytosis / apical part of cell / synaptic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / ATPase binding / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / postsynaptic membrane / early endosome / lysosome / endosome membrane / endosome / nuclear speck / cilium / apical plasma membrane / Golgi membrane / axon / lysosomal membrane / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding
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 transmembrane spanning segment / Renin receptor N-terminal domain / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal ...ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / : / Renin receptor-like transmembrane spanning segment / Renin receptor N-terminal domain / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / : / V-type proton ATPase subunit f-like / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / Renin receptor / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 ...Uncharacterized protein / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / Renin receptor / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / V-type proton ATPase subunit F / Type IV secretion protein Dot / Ribonuclease kappa / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit H / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human) / Legionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang L / Wu H
CitationJournal: Mol Cell / Year: 2020
Title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Authors: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu /
Abstract: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.
History
DepositionApr 20, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wm4
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wm4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21849.png

Downloads & links

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Map

FileDownload / File: emd_21849.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman V-ATPase in state 3 (composite map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7 / Movie #1: 3.7
Minimum - Maximum-13.677958500000001 - 27.491752999999999
Average (Standard dev.)0.016995996 (±1.1574208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-13.67827.4920.017

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Supplemental data

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Additional map: Human V-ATPase in state 3

Fileemd_21849_additional_1.map
AnnotationHuman V-ATPase in state 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human V-ATPase with SidK and ADP

EntireName: Human V-ATPase with SidK and ADP
Components
  • Complex: Human V-ATPase with SidK and ADP
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G 1
    • Protein or peptide: V-type proton ATPase subunit e 1
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: SidK
    • 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 S1
    • Protein or peptide: Renin receptor
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: V-type proton ATPase subunit H
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human V-ATPase with SidK and ADP

SupramoleculeName: Human V-ATPase with SidK and ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: V-type proton ATPase 116 kDa subunit a isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.512414 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 MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSTVFS GRYIILLMGV FSMYTGLIYN DCFSKSLNIF GSSWS VRPM FTYNWTEETL RGNPVLQLNP ALPGVFGGPY PFGIDPIWNI ATNKLTFLNS FKMKMSVILG IIHMLFGVSL SLFNHI YFK KPLNIYFGFI PEIIFMTSLF GYLVILIFYK WTAYDAHTSE NAPSLLIHFI NMFLFSYPES GYSMLYSGQK GIQCFLV VV ALLCVPWMLL FKPLVLRRQY LRRKHLGTLN FGGIRVGNGP TEEDAEIIQH DQLSTHSEDA DEPSEDEVFD FGDTMVHQ A IHTIEYCLGC ISNTASYLRL WALSLAHAQL SEVLWTMVIH IGLSVKSLAG GLVLFFFFTA FATLTVAILL IMEGLSAFL HALRLHWVEF QNKFYSGTGF KFLPFSFEHI REGKFEE

UniProtKB: V-type proton ATPase 116 kDa subunit a 1

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Macromolecule #2: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.9995 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATSKNN NLAVTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATSKNN NLAVTSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLANGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE IVKKDDFVLD SEYLVTLLVV VPKLNHNDWI KQYETLAEMV VPRSSNVLSE DQDSYLCNVT LFRKAVDDFR HK ARENKFI VRDFQYNEEE MKADKEEMNR LSTDKKKQFG PLVRWLKVNF SEAFIAWIHV KALRVFVESV LRYGLPVNFQ AML LQPNKK TLKKLREVLH ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

UniProtKB: V-type proton ATPase subunit C 1

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

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.183346 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID QESYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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Macromolecule #4: V-type proton ATPase subunit G 1

MacromoleculeName: V-type proton ATPase subunit G 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.781547 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSRGSCS TEVEKETQEK MTILQTYFR QNRDEVLDNL LAFVCDIRPE IHENYRING

UniProtKB: V-type proton ATPase subunit G 1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.380329 KDa
SequenceString:
MAYHGLTVPL IVMSVFWGFV GFLVPWFIPK GPNRGVIITM LVTCSVCCYL FWLIAILAQL NPLFGPQLKN ETIWYLKYHW P

UniProtKB: V-type proton ATPase subunit e 1

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Macromolecule #6: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.43522 KDa
SequenceString:
MGWLRPGPRP LCPPARASWA FSHRFPSPLA PRRSPTPFFM ASLLCCGPKL AACGIVLSAW GVIMLIMLGI FFNVHSAVLI EDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRLN KRKEYMVR

UniProtKB: Ribonuclease kappa

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Macromolecule #7: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.379875 KDa
SequenceString: MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML ...String:
MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML PPRNRGTVTY IAPPGNYDTS DVVLELEFEG VKEKFTMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERGNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MADSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVS IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM IAFYDMARRA VETTAQ SDN KITWSIIREH MGDILYKLSS MKFKDPLKDG EAKIKSDYAQ LLEDMQNAFR SLED

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #8: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.5615 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TGGPAVGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TGGPAVGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE MIQTGISAID GMNSIARGQK IPIFSAAGLP HNEIAAQICR QAGLVKKSKD VVDYSEENFA IVFAAMGVNM ET ARFFKSD FEENGSMDNV CLFLNLANDP TIERIITPRL ALTTAEFLAY QCEKHVLVIL TDMSSYAEAL REVSAAREEV PGR RGFPGY MYTDLATIYE RAGRVEGRNG SITQIPILTM PNDDITHPIP DLTGYITEGQ IYVDRQLHNR QIYPPINVLP SLSR LMKSA IGEGMTRKDH ADVSNQLYAC YAIGKDVQAM KAVVGEEALT SDDLLYLEFL QKFERNFIAQ GPYENRTVFE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

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

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Macromolecule #9: SidK

MacromoleculeName: SidK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 65.505297 KDa
SequenceString: MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI ...String:
MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI TEDNEGINQL FKLGLHLLAM ANEKIDEQYH LFKGYVKDQP EESPFEGILP AEDQKILVKT MIDYAMPKLS SK VLQDKLS ALSSSDVLTK TLLDSIDRIV KENEKLNALS KVKLGKFGLD IREIEVIYSQ ALKISPQDAL QYTAQQCDAQ LLS MAFPDS QNYIIESISN KKVKTIAELI HSKEFIYQII KTEVFKQVDP NEKIRLQAAT ELYQLLGRIM DKQINLFTKM NLEQ INEYI QTKTKAILDK IPERVELLTF MGFEIPTFKG IETLMTDISH SQDNETLAIA QEFYTNIKNA KNQLLGDKLI EDITP QDVE KFFNQCSQYG SEAAEKLADN RPVLTKIADI LTAIARWAIS LIGFNTPPQF LAPTRTCVDQ VSDEITKIKL KLEDTL GSL QKVQEESLSL

UniProtKB: Uncharacterized protein

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Macromolecule #10: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.311918 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 KKILKEKSEK DLEQRRAAGE VLEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #11: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.38821 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQQSIPAVL EIPSKEHPYD AAKDSILRRA RGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #12: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.06748 KDa
SequenceString: MMAAMATARV RMGPRCAQAL WRMPWLPVFL SLAAAAAAAA AEQQVPLVLW SSDRDLWAPA ADTHEGHITS DLQLSTYLDP ALELGPRNV LLFLQDKLSI EDFTAYGGVF GNKQDSAFSN LENALDLAPS SLVLPAVDWY AVSTLTTYLQ EKLGASPLHV D LATLRELK ...String:
MMAAMATARV RMGPRCAQAL WRMPWLPVFL SLAAAAAAAA AEQQVPLVLW SSDRDLWAPA ADTHEGHITS DLQLSTYLDP ALELGPRNV LLFLQDKLSI EDFTAYGGVF GNKQDSAFSN LENALDLAPS SLVLPAVDWY AVSTLTTYLQ EKLGASPLHV D LATLRELK LNASLPALLL IRLPYTASSG LMAPREVLTG NDEVIGQVLS TLKSEDVPYT AALTAVRPSR VARDVAVVAG GL GRQLLQK QPVSPVIHPP VSYNDTAPRI LFWAQNFSVA YKDQWEDLTP LTFGVQELNL TGSFWNDSFA RLSLTYERLF GTT VTFKFI LANRLYPVSA RHWFTMERLE VHSNGSVAYF NASQVTGPSI YSFHCEYVSS LSKKGSLLVA RTQPSPWQMM LQDF QIQAF NVMGEQFSYA SDCASFFSPG IWMGLLTSLF MLFIFTYGLH MILSLKTMDR FDDHKGPTIS LTQIV

UniProtKB: V-type proton ATPase subunit S1

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Macromolecule #13: Renin receptor

MacromoleculeName: Renin receptor / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.045855 KDa
SequenceString: MAVFVVLLAL VAGVLGNEFS ILKSPGSVVF RNGNWPIPGE RIPDVAALSM GFSVKEDLSW PGLAVGNLFH RPRATVMVMV KGVNKLALP PGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLSV TLRQLRNRLF Q ENSVLSSL ...String:
MAVFVVLLAL VAGVLGNEFS ILKSPGSVVF RNGNWPIPGE RIPDVAALSM GFSVKEDLSW PGLAVGNLFH RPRATVMVMV KGVNKLALP PGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLSV TLRQLRNRLF Q ENSVLSSL PLNSLSRNNE VDLLFLSELQ VLHDISSLLS RHKHLAKDHS PDLYSLELAG LDEIGKRYGE DSEQFRDASK IL VDALQKF ADDMYSLYGG NAVVELVTVK SFDTSLIRKT RTILEAKQAK NPASPYNLAY KYNFEYSVVF NMVLWIMIAL ALA VIITSY NIWNMDPGYD SIIYRMTNQK IRMD

UniProtKB: Renin receptor

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Macromolecule #14: V-type proton ATPase 21 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.418213 KDa
SequenceString: MTGLALLYSG VFVAFWACAL AVGVCYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLALLYSG VFVAFWACAL AVGVCYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

UniProtKB: V-type proton ATPase 21 kDa proteolipid subunit c''

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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: Homo sapiens (human)
Molecular weightTheoretical: 15.743655 KDa
SequenceString:
MSESKSGPEY ASFFAVMGAS AAMVFSALGA AYGTAKSGTG IAAMSVMRPE QIMKSIIPVV MAGIIAIYGL VVAVLIANSL NDDISLYKS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

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

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Macromolecule #16: V-type proton ATPase subunit d 1

MacromoleculeName: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

UniProtKB: V-type proton ATPase subunit d 1

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Macromolecule #17: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.949949 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHICKEQT VQYILTMVDD MLQENHQRVS IFFDYARCSK NTAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSPE EKQEMLQTEG SQCAKTFINL MTHICKEQT VQYILTMVDD MLQENHQRVS IFFDYARCSK NTAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLSSQKLR GSGVAVETGT VSSSDSSQYV QCVAGCLQLM LRVNEYRFAW VEADGVNCIM GVLSNKCGFQ LQ YQMIFSI WLLAFSPQMC EHLRRYNIIP VLSDILQESV KEKVTRIILA AFRNFLEKST ERETRQEYAL AMIQCKVLKQ LEN LEQQKY DDEDISEDIK FLLEKLGESV QDLSSFDEYS SELKSGRLEW SPVHKSEKFW RENAVRLNEK NYELLKILTK LLEV SDDPQ VLAVAAHDVG EYVRHYPRGK RVIEQLGGKQ LVMNHMHHED QQVRYNALLA VQKLMVHNWE YLGKQLQSEQ PQTAA ARS

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #18: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 18 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 19 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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