[English] 日本語
Yorodumi
- EMDB-21844: The Vo region of human V-ATPase in state 1 (focused refinement) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21844
TitleThe Vo region of human V-ATPase in state 1 (focused refinement)
Map dataThe Vo region of human V-ATPase in state 1 (focused refinement)
Sample
  • Complex: Human V-ATPase with SidK
    • Protein or peptide: x 8 types
  • Ligand: x 7 types
KeywordsV-ATPase / proton pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / eye pigmentation / central nervous system maturation / ATPase-coupled ion transmembrane transporter activity / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning ...proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / eye pigmentation / central nervous system maturation / ATPase-coupled ion transmembrane transporter activity / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / Transferrin endocytosis and recycling / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosome to plasma membrane protein transport / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / osteoclast development / ROS and RNS production in phagocytes / dendritic spine membrane / regulation of cellular pH / azurophil granule membrane / tertiary granule membrane / ATPase activator activity / regulation of MAPK cascade / ficolin-1-rich granule membrane / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / RHOA GTPase cycle / regulation of macroautophagy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / axon terminus / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton transmembrane transport / receptor-mediated endocytosis / secretory granule membrane / transmembrane transport / small GTPase binding / synaptic vesicle membrane / phagocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / early endosome / lysosome / endosome membrane / nuclear speck / apical plasma membrane / Golgi membrane / axon / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
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 protein / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 ...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, 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-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit e 1 / Renin receptor / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / Ribonuclease kappa / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase 21 kDa proteolipid subunit c''
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wlw
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21844.png

Downloads & links

-
Map

FileDownload / File: emd_21844.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe Vo region of human V-ATPase in state 1 (focused refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.6245896 - 3.4699976
Average (Standard dev.)0.0033026803 (±0.068116285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.6253.4700.003

-
Supplemental data

-
Sample components

+
Entire : Human V-ATPase with SidK

EntireName: Human V-ATPase with SidK
Components
  • Complex: Human V-ATPase with SidK
    • 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 116 kDa subunit a isoform 1
    • Protein or peptide: V-type proton ATPase subunit e 1
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: Renin receptor
  • Ligand: tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
  • 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

+
Supramolecule #1: Human V-ATPase with SidK

SupramoleculeName: Human V-ATPase with SidK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: V-type proton ATPase 21 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit / type: protein_or_peptide / ID: 1 / 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''

+
Macromolecule #2: V-type proton ATPase 16 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit / type: protein_or_peptide / ID: 2 / 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

+
Macromolecule #3: V-type proton ATPase subunit d 1

MacromoleculeName: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 3 / 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

+
Macromolecule #4: 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: 4 / 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

+
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

+
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

+
Macromolecule #7: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 7 / 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

+
Macromolecule #8: Renin receptor

MacromoleculeName: Renin receptor / type: protein_or_peptide / ID: 8 / 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

+
Macromolecule #13: tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-...

MacromoleculeName: tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium
type: ligand / ID: 13 / Number of copies: 10 / Formula: WSS
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-WSS:
tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium

+
Macromolecule #14: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 14 / Number of copies: 13 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #15: (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-...

MacromoleculeName: (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid
type: ligand / ID: 15 / Number of copies: 1 / Formula: WJS
Molecular weightTheoretical: 497.391 Da
Chemical component information

ChemComp-WJS:
(2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid

+
Macromolecule #16: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 16 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

+
Macromolecule #17: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

MacromoleculeName: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / type: ligand / ID: 17 / Number of copies: 1 / Formula: PSF
Molecular weightTheoretical: 455.437 Da
Chemical component information

ChemComp-PSF:
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

+
Macromolecule #18: 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: 18 / 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 #19: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 19 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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