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- EMDB-27984: Yeast VO in complex with Vma12-22p -

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Basic information

Entry
Database: EMDB / ID: EMD-27984
TitleYeast VO in complex with Vma12-22p
Map data
Sample
  • Complex: Yeast Vo in complex with Vma12-22p
    • Protein or peptide: x 11 types
Function / homology
Function and homology information


Vma12-Vma22 assembly complex / extrinsic component of endoplasmic reticulum membrane / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling ...Vma12-Vma22 assembly complex / extrinsic component of endoplasmic reticulum membrane / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / protein targeting to vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuole organization / fungal-type vacuole / vacuolar acidification / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / RNA endonuclease activity / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / unfolded protein binding / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / Golgi membrane / endoplasmic reticulum membrane / membrane / nucleus
Similarity search - Function
Vma22/CCDC115 / 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, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic ...Vma22/CCDC115 / 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, V1 complex, subunit F, eukaryotic / 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 F / ATPase, V1 complex, subunit F superfamily / 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
V-type proton ATPase subunit F / V-type proton ATPase subunit f / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit c' / Vacuolar ATPase assembly protein VMA22 / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang H / Bueler SA / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of V-ATPase V region assembly by Vma12p, 21p, and 22p.
Authors: Hanlin Wang / Stephanie A Bueler / John L Rubinstein /
Abstract: Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a ...Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V region and a membrane-embedded proton-translocating V region. V is assembled in the endoplasmic reticulum (ER) membrane, and V is assembled in the cytosol. However, V binds V only after V is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated V complexes and subcomplexes from bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of V while blocking premature binding of V. Vma21p, which contains an ER-retrieval motif, binds the V:Vma12-22p complex, "mature" V, and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V with V removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of V-ATPase V0 region assembly by Vma12p, 21p, and 22p
Authors: Wang H / Bueler SA / Rubinstein JL
History
DepositionAug 29, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27984.png

Downloads & links

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Map

FileDownload / File: emd_27984.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-6.486403 - 12.719189
Average (Standard dev.)0.007470909 (±0.31088462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27984_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27984_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast Vo in complex with Vma12-22p

EntireName: Yeast Vo in complex with Vma12-22p
Components
  • Complex: Yeast Vo in complex with Vma12-22p
    • Protein or peptide: Vacuolar ATPase assembly protein VMA22
    • Protein or peptide: V-type proton ATPase assembly factor Vma12p
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Yeast V-ATPase subunit f
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit c'

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Supramolecule #1: Yeast Vo in complex with Vma12-22p

SupramoleculeName: Yeast Vo in complex with Vma12-22p / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vacuolar ATPase assembly protein VMA22

MacromoleculeName: Vacuolar ATPase assembly protein VMA22 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 21.104717 KDa
SequenceString:
MSETRMAQNM DTTDEQYLRL IELLSNYDST LEQLQKGFQD GYIQLSRSNY YNKDSLRGNY GEDYWDETYI GQLMATVEEK NSKVVVEIV KRKAQDKQEK KEEEDNKLTQ RKKGTKPEKQ KTQSHKLKQD YDPILMFGGV LSVPSSLRQS QTSFKGCIPL I AQLINYKN EILTLVETLS EQE

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Macromolecule #2: V-type proton ATPase assembly factor Vma12p

MacromoleculeName: V-type proton ATPase assembly factor Vma12p / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 16.460309 KDa
SequenceString: MFEIKLNDRI TEFLRKFKNS AKSNEGIDED IDLFLKRHAI PMQSLLFYVK EYRKDSDLQC SIKELLKPLE FEFKPKAVRG LHYSEDFKK KLEFLKYQEQ ELEYQSMVK(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...String:
MFEIKLNDRI TEFLRKFKNS AKSNEGIDED IDLFLKRHAI PMQSLLFYVK EYRKDSDLQC SIKELLKPLE FEFKPKAVRG LHYSEDFKK KLEFLKYQEQ ELEYQSMVK(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 13.47917 KDa
SequenceString:
MAEKRTLIAV IADEDTTTGL LLAGIGQITP ETQEKNFFVY QEGKTTKEEI TDKFNHFTEE RDDIAILLIN QHIAENIRAR VDSFTNAFP AILEIPSKDH PYDPEKDSVL KRVRKLFGE

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Macromolecule #4: V-type proton ATPase subunit a, vacuolar isoform

MacromoleculeName: V-type proton ATPase subunit a, vacuolar isoform / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 95.625484 KDa
SequenceString: MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM ...String:
MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM IDANGENIAA AIGASVNYVT GVIARDKVAT LEQILWRVLR GNLFFKTVEI EQPVYDVKTR EYKHKNAFIV FS HGDLIIK RIRKIAESLD ANLYDVDSSN EGRSQQLAKV NKNLSDLYTV LKTTSTTLES ELYAIAKELD SWFQDVTREK AIF EILNKS NYDTNRKILI AEGWIPRDEL ATLQARLGEM IARLGIDVPS IIQVLDTNHT PPTFHRTNKF TAGFQSICDC YGIA QYREI NAGLPTIVTF PFMFAIMFGD MGHGFLMTLA ALSLVLNEKK INKMKRGEIF DMAFTGRYII LLMGVFSMYT GFLYN DIFS KTMTIFKSGW KWPDHWKKGE SITATSVGTY PIGLDWAWHG TENALLFSNS YKMKLSILMG FIHMTYSYFF SLANHL YFN SMIDIIGNFI PGLLFMQGIF GYLSVCIVYK WAVDWVKDGK PAPGLLNMLI NMFLSPGTID DELYPHQAKV QVFLLLM AL VCIPWLLLVK PLHFKFTHKK KSHEPLPSTE ADASSEDLEA QQLISAMDAD DAEEEEVGSG SHGEDFGDIM IHQVIHTI E FCLNCVSHTA SYLRLWALSL AHAQLSSVLW TMTIQIAFGF RGFVGVFMTV ALFAMWFALT CAVLVLMEGT SAMLHSLRL HWVESMSKFF VGEGLPYEPF AFEYKDMEVA VASASSSASS

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Macromolecule #5: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 29.694885 KDa
SequenceString: MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK ...String:
MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK SGDNLTVVIN SLGWAFEDED GDDEYATEET LSHHDNNKGK EGDDDILSSI WTEGLLMCLI VSALLLFILI VA LSWISNL DITYGALEKS TNPIKKNN

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Macromolecule #6: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 22.610641 KDa
SequenceString: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...String:
MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ

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Macromolecule #7: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 39.822484 KDa
SequenceString: MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT ...String:
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT AEELDDMNIE IIRNKLYKAY LEDFYNFVTE EIPEPAKECM QTLLGFEADR RSINIALNSL QSSDIDPDLK SD LLPNIGK LYPLATFHLA QAQDFEGVRA ALANVYEYRG FLETGNLEDH FYQLEMELCR DAFTQQFAIS TVWAWMKSKE QEV RNITWI AECIAQNQRE RINNYISVY

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Macromolecule #8: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 8.387065 KDa
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE FAE

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Macromolecule #9: Yeast V-ATPase subunit f

MacromoleculeName: Yeast V-ATPase subunit f / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 9.369934 KDa
SequenceString:
MRPVVSTGKA WCCTVLSAFG VVILSVIAHL FNTNHESFVG SINDPEDGPA VAHTVYLAAL VYLVFFVFCG FQVYLARRKP SIELR

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Macromolecule #10: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 10 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 16.357501 KDa
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV C

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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: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 17.046361 KDa
SequenceString:
MSTQLASNIY APLYAPFFGF AGCAAAMVLS CLGAAIGTAK SGIGIAGIGT FKPELIMKSL IPVVMSGILA IYGLVVAVLI AGNLSPTED YTLFNGFMHL SCGLCVGFAC LSSGYAIGMV GDVGVRKYMH QPRLFVGIVL ILIFSEVLGL YGMIVALILN T RGSE

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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
GridModel: Homemade / Material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 308537

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