[English] 日本語
Yorodumi
- EMDB-44350: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44350
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Map data
Sample
  • Complex: Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo
    • Protein or peptide: x 7 types
  • Protein or peptide: x 4 types
  • Ligand: x 6 types
KeywordsMembrane / Synaptic / Complex / PROTON TRANSPORT
Function / homology
Function and homology information


regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity ...regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / intracellular organelle / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / osteoclast development / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / vacuolar acidification / ROS and RNS production in phagocytes / Neutrophil degranulation / regulation of synaptic vesicle exocytosis / cholesterol binding / : / regulation of neuronal synaptic plasticity / presynaptic active zone / response to amyloid-beta / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / synaptic vesicle endocytosis / excitatory synapse / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / axon terminus / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / SH2 domain binding / receptor-mediated endocytosis / SNARE binding / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / Schaffer collateral - CA1 synapse / terminal bouton / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / endocytosis / melanosome / synaptic vesicle / ATPase binding / presynapse / signaling receptor activity / presynaptic membrane / cell body / postsynaptic membrane / intracellular iron ion homeostasis / positive regulation of ERK1 and ERK2 cascade / endosome / receptor-mediated endocytosis of virus by host cell / endosome membrane / postsynaptic density / early endosome / lysosome / neuron projection / apical plasma membrane / protein domain specific binding / external side of plasma membrane / axon / lysosomal membrane / centrosome / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane
Similarity search - Function
Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / 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 ...Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like protein / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / 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-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit / Renin receptor / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCoupland CE / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Science / Year: 2024
Title: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Authors: Claire E Coupland / Ryan Karimi / Stephanie A Bueler / Yingke Liang / Gautier M Courbon / Justin M Di Trani / Cassandra J Wong / Rayan Saghian / Ji-Young Youn / Lu-Yang Wang / John L Rubinstein /
Abstract: Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or ...Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.
History
DepositionMar 31, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44350.png

Downloads & links

-
Map

FileDownload / File: emd_44350.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-1.188712 - 1.723616
Average (Standard dev.)0.000970846 (±0.050110538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_44350_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44350_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo

EntireName: Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo
Components
  • Complex: Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo
    • Protein or peptide: ATPase H+-transporting V1 subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: Synaptophysin
    • Protein or peptide: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: Renin receptor
  • Protein or peptide: V-type proton ATPase subunit S1
  • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
  • Protein or peptide: V-type proton ATPase subunit e 2
  • Protein or peptide: Rnasek protein
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CHOLESTEROL

+
Supramolecule #1: Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo

SupramoleculeName: Synaptic vesicle V-ATPase with synaptophysin and SidK, state 3, Vo
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #11, #3, #5-#6, #9-#10
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague Dawley / Organ: Brain / Organelle: Synaptic Vesicle / Location in cell: Synaptic Vesicle Membrane

+
Macromolecule #1: ATPase H+-transporting V1 subunit D

MacromoleculeName: ATPase H+-transporting V1 subunit D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 28.35902 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 KKIIKEKSEK DLERRRAAGE VMEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

+
Macromolecule #2: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 51.160359 KDa
SequenceString: MMAATVVSRI RTGTRWAPVL WLLLSLVAVA AAVAAEQQVP LVLWSSDRDL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ...String:
MMAATVVSRI RTGTRWAPVL WLLLSLVAVA AAVAAEQQVP LVLWSSDRDL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ALLLIRLPYT ASSGLMAPRE VLTGNDEVIG QVLSTLESED VPYTAALTAV RPSRVARDVA MVAGGLGRQL LQ TQVASPA IHPPVSYNDT APRILFWAQN FSVAYKDEWK DLTSLTFGVE NLNLTGSFWN DSFAMLSLTY EPLFGATVTF KFI LASRFY PVSARYWFTM ERLEIHSNGS VAHFNVSQVT GPSIYSFHCE YVSSLSKKGS LLVTNVPSLW QMTLHNFQIQ AFNV TGEQF SYASDCAGFF SPGIWMGLLT TLFMLFIFTY GLHMILSLKT MDRFDDRKGP TITLTQIV

UniProtKB: V-type proton ATPase subunit S1

+
Macromolecule #3: Synaptophysin

MacromoleculeName: Synaptophysin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 33.331523 KDa
SequenceString: MDVVNQLVAG GQFRVVKEPL GFVKVLQWVF AIFAFATCGS YTGELRLSVE CANKTESALN IEVEFEYPFR LHQVYFDAPS CVKGGTTKI FLVGDYSSSA EFFVTVAVFA FLYSMGALAT YIFLQNKYRE NNKGPMMDFL ATAVFAFMWL VSSSAWAKGL S DVKMATDP ...String:
MDVVNQLVAG GQFRVVKEPL GFVKVLQWVF AIFAFATCGS YTGELRLSVE CANKTESALN IEVEFEYPFR LHQVYFDAPS CVKGGTTKI FLVGDYSSSA EFFVTVAVFA FLYSMGALAT YIFLQNKYRE NNKGPMMDFL ATAVFAFMWL VSSSAWAKGL S DVKMATDP ENIIKEMPMC RQTGNTCKEL RDPVTSGLNT SVVFGFLNLV LWVGNLWFVF KETGWAAPFM RAPPGAPEKQ PA PGDAYGD AGYGQGPGGY GPQDSYGPQG GYQPDYGQPA SGGGGYGPQG DYGQQGYGQQ GAPTSFSNQM

UniProtKB: Synaptophysin

+
Macromolecule #4: V-type proton ATPase 116 kDa subunit a 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 94.950836 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTHGFQN IVDAYGIGTY REINPAPYTV ITFP FLFAV MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSMVFS GRYIILLMGL FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FTIGNWTEET LLGSSVLQLN PAIPGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMLFGVS LSLFNH IYF KKPLNIYFGF IPEIIFMSSL FGYLVILIFY KWTAYDAHSS RNAPSLLIHF INMFLFSYPE SGNAMLYSGQ KGIQCFL IV VAMLCVPWML LFKPLILRHQ YLRKKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLHVRSLA GGLGLFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYTGTG FKFLPF

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

+
Macromolecule #5: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

MacromoleculeName: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 21.618553 KDa
SequenceString: MTGLELLYLG IFVAFWACMI VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLELLYLG IFVAFWACMI VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

UniProtKB: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

+
Macromolecule #6: V-type proton ATPase subunit

MacromoleculeName: V-type proton ATPase subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 40.341934 KDa
SequenceString: MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI ...String:
MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV 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

+
Macromolecule #7: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.20302 KDa
SequenceString:
MTAHSFALPV IIFTTFWGLI GIAGPWFVPK GPNRGVIITM LVATAVCCYL FWLIAILAQL NPLFGPQLKN ETIWYVRFLW E

UniProtKB: V-type proton ATPase subunit e 2

+
Macromolecule #8: Rnasek protein

MacromoleculeName: Rnasek protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.502132 KDa
SequenceString:
LCCGPKLAAC GIVLSAWGVI MLIMLGIFFN VHSAVLIEDV PFTEKDFENG PQNIYNLYEQ VSYNCFIAAG LYLLLGGFSF CQVRLN

UniProtKB: Rnasek protein

+
Macromolecule #9: V-type proton ATPase 16 kDa proteolipid subunit c

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit c / type: protein_or_peptide / ID: 9 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 15.815833 KDa
SequenceString:
MADIKNNPEY SSFFGVMGAS SAMVFSAMGA AYGTAKSGTG IAAMSVMRPE LIMKSIIPVV MAGIIAIYGL VVAVLIANSL TDGITLYRS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

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

+
Macromolecule #10: Renin receptor

MacromoleculeName: Renin receptor / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 39.118578 KDa
SequenceString: MAVLVVLLSS LVSSALANEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVT VKGVDKLAL PTGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLNS ...String:
MAVLVVLLSS LVSSALANEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVT VKGVDKLAL PTGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLNS LPLNSLSRNN EVDLLFLSEL QVLHDISSLL SRHKHLAKDH SPDLYSLELA GLDELGKRYG EDSEQFRDAS RI LVDALQK FADDMYSLYG GNAVVELVTV KSFDTSLVRK SRTILETKQE NTQSPYNLAY KYNLEYSVVF NLVLWIMTGL ALA VIITSY NIWNMDPGYD SIIYRMTNQK IRMD

UniProtKB: Renin receptor

+
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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 13.389262 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA KGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

+
Macromolecule #14: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 14 / Number of copies: 5 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

+
Macromolecule #15: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-t...

MacromoleculeName: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate
type: ligand / ID: 15 / Number of copies: 1 / Formula: WJP
Molecular weightTheoretical: 534.603 Da
Chemical component information

ChemComp-WJP:
methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate

+
Macromolecule #16: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 16 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
Macromolecule #17: (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAH...

MacromoleculeName: (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 17 / Number of copies: 1 / Formula: LP3
Molecular weightTheoretical: 524.691 Da
Chemical component information

ChemComp-LP3:
(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE

+
Macromolecule #18: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 18 / Number of copies: 9 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #19: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 19 / Number of copies: 30 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Homemade / Material: GRAPHENE OXIDE / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 37.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198533
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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