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- EMDB-21896: Full-length human ENaC ECD -

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Basic information

Entry
Database: EMDB / ID: EMD-21896
TitleFull-length human ENaC ECD
Map dataENaC_FL sharpened EM map (Bfactor -101.4)
Sample
  • Complex: Full-length human ENaC heterotrimer bound with two high-affinity Fabs
    • Protein or peptide: Amiloride-sensitive sodium channel subunit alphaEpithelial sodium channel
    • Protein or peptide: Amiloride-sensitive sodium channel subunit betaEpithelial sodium channel
    • Protein or peptide: Amiloride-sensitive sodium channel subunit gammaEpithelial sodium channel
    • Protein or peptide: 7B1 Fab
    • Protein or peptide: 10D4 Fab
  • Ligand: SODIUM IONSodium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex ...: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex / sperm principal piece / ligand-gated sodium channel activity / epithelial fluid transport / sodium ion homeostasis / artery smooth muscle contraction / mucus secretion / neutrophil activation involved in immune response / WW domain binding / cellular response to aldosterone / cellular response to acidic pH / multicellular organismal-level water homeostasis / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / potassium ion homeostasis / sodium channel activity / motile cilium / erythrocyte homeostasis / response to food / ciliary membrane / sodium ion transport / sodium ion transmembrane transport / acrosomal vesicle / multicellular organism growth / cytoplasmic vesicle membrane / Stimuli-sensing channels / regulation of blood pressure / monoatomic ion channel activity / gene expression / response to xenobiotic stimulus / apical plasma membrane / external side of plasma membrane / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Amiloride-sensitive sodium channel subunit alpha / Amiloride-sensitive sodium channel subunit beta / Amiloride-sensitive sodium channel subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsPosert R / Baconguis I / Noreng S / Bharadwaj A / Houser A
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD017871 United States
American Heart Association18PRE33990205 United States
American Heart Association19TPA34760754 United States
National Science Foundation (NSF, United States)DGE-1937961 United States
CitationJournal: Elife / Year: 2020
Title: Molecular principles of assembly, activation, and inhibition in epithelial sodium channel.
Authors: Sigrid Noreng / Richard Posert / Arpita Bharadwaj / Alexandra Houser / Isabelle Baconguis /
Abstract: The molecular bases of heteromeric assembly and link between Na self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated ...The molecular bases of heteromeric assembly and link between Na self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated that ENaC subunits - α, β, and γ - assemble in a counterclockwise configuration when viewed from outside the cell with the protease-sensitive GRIP domains in the periphery (Noreng et al., 2018). Here we describe the structure of ENaC resolved by cryo-electron microscopy at 3 Å. We find that a combination of precise domain arrangement and complementary hydrogen bonding network defines the subunit arrangement. Furthermore, we determined that the α subunit has a primary functional module consisting of the finger and GRIP domains. The module is bifurcated by the α2 helix dividing two distinct regulatory sites: Na and the inhibitory peptide. Removal of the inhibitory peptide perturbs the Na site via the α2 helix highlighting the critical role of the α2 helix in regulating ENaC function.
History
DepositionMay 2, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.482
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.482
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wth
  • Surface level: 0.482
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21896.png

Downloads & links

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Map

FileDownload / File: emd_21896.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationENaC_FL sharpened EM map (Bfactor -101.4)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.482 / Movie #1: 0.482
Minimum - Maximum-1.208659 - 2.3689759
Average (Standard dev.)0.004876746 (±0.054992843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z318.720318.720318.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.2092.3690.005

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Supplemental data

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Mask #1

Fileemd_21896_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ENaC FL unsharpened EM map

Fileemd_21896_additional.map
AnnotationENaC_FL unsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ENaC FL EM half map A

Fileemd_21896_half_map_1.map
AnnotationENaC_FL EM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ENaC FL EM half map B

Fileemd_21896_half_map_2.map
AnnotationENaC_FL EM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length human ENaC heterotrimer bound with two high-affinity Fabs

EntireName: Full-length human ENaC heterotrimer bound with two high-affinity Fabs
Components
  • Complex: Full-length human ENaC heterotrimer bound with two high-affinity Fabs
    • Protein or peptide: Amiloride-sensitive sodium channel subunit alphaEpithelial sodium channel
    • Protein or peptide: Amiloride-sensitive sodium channel subunit betaEpithelial sodium channel
    • Protein or peptide: Amiloride-sensitive sodium channel subunit gammaEpithelial sodium channel
    • Protein or peptide: 7B1 Fab
    • Protein or peptide: 10D4 Fab
  • Ligand: SODIUM IONSodium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Full-length human ENaC heterotrimer bound with two high-affinity Fabs

SupramoleculeName: Full-length human ENaC heterotrimer bound with two high-affinity Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T/17 / Recombinant plasmid: pBacMam
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Amiloride-sensitive sodium channel subunit alpha

MacromoleculeName: Amiloride-sensitive sodium channel subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.780531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGNKLEEQD SSPPQSTPGL MKGNKREEQG LGPEPAAPQQ PTAEEEALIE FHRSYRELFE FFCNNTTIHG AIRLVCSQHN RMKTAFWAV LWLCTFGMMY WQFGLLFGEY FSYPVSLNIN LNSDKLVFPA VTICTLNPYR YPEIKEELEE LDRITEQTLF D LYKYSSFT ...String:
MEGNKLEEQD SSPPQSTPGL MKGNKREEQG LGPEPAAPQQ PTAEEEALIE FHRSYRELFE FFCNNTTIHG AIRLVCSQHN RMKTAFWAV LWLCTFGMMY WQFGLLFGEY FSYPVSLNIN LNSDKLVFPA VTICTLNPYR YPEIKEELEE LDRITEQTLF D LYKYSSFT TLVAGSRSRR DLRGTLPHPL QRLRVPPPPH GARRARSVAS SLRDNNPQVD WKDWKIGFQL CNQNKSDCFY QT YSSGVDA VREWYRFHYI NILSRLPETL PSLEEDTLGN FIFACRFNQV SCNQANYSHF HHPMYGNCYT FNDKNNSNLW MSS MPGINN GLSLMLRAEQ NDFIPLLSTV TGARVMVHGQ DEPAFMDDGG FNLRPGVETS ISMRKETLDR LGGDYGDCTK NGSD VPVEN LYPSKYTQQV CIHSCFQESM IKECGCAYIF YPRPQNVEYC DYRKHSSWGY CYYKLQVDFS SDHLGCFTKC RKPCS VTSY QLSAGYSRWP SVTSQEWVFQ MLSRQNNYTV NNKRNGVAKV NIFFKELNYK TNSESPSVTM VTLLSNLGSQ WSLWFG SSV LSVVEMAELV FDLLVIMFLM LLRRFRSRYW SPGRGGRGAQ EVASTLASSP PSHFCPHPMS LSLSQPGPAP SPALTAP PP AYATLGPRPS PGGSAGASSS TCPLGGP

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Macromolecule #2: Amiloride-sensitive sodium channel subunit beta

MacromoleculeName: Amiloride-sensitive sodium channel subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.728891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHVKKYLLKG LHRLQKGPGY TYKELLVWYC DNTNTHGPKR IICEGPKKKA MWFLLTLLFA ALVCWQWGIF IRTYLSWEVS VSLSVGFKT MDFPAVTICN ASPFKYSKIK HLLKDLDELM EAVLERILAP ELSHANATRN LNFSIWNHTP LVLIDERNPH H PMVLDLFG ...String:
MHVKKYLLKG LHRLQKGPGY TYKELLVWYC DNTNTHGPKR IICEGPKKKA MWFLLTLLFA ALVCWQWGIF IRTYLSWEVS VSLSVGFKT MDFPAVTICN ASPFKYSKIK HLLKDLDELM EAVLERILAP ELSHANATRN LNFSIWNHTP LVLIDERNPH H PMVLDLFG DNHNGLTSSS ASEKICNAHG CKMAMRLCSL NRTQCTFRNF TSATQALTEW YILQATNIFA QVPQQELVEM SY PGEQMIL ACLFGAEPCN YRNFTSIFYP HYGNCYIFNW GMTEKALPSA NPGTEFGLKL ILDIGQEDYV PFLASTAGVR LML HEQRSY PFIRDEGIYA MSGTETSIGV LVDKLQRMGE PYSPCTVNGS EVPVQNFYSD YNTTYSIQAC LRSCFQDHMI RNCN CGHYL YPLPRGEKYC NNRDFPDWAH CYSDLQMSVA QRETCIGMCK ESCNDTQYKM TISMADWPSE ASEDWIFHVL SQERD QSTN ITLSRKGIVK LNIYFQEFNY RTIEESAANN IVWLLSNLGG QFGFWMGGSV LCLIEFGEII IDFVWITIIK LVALAK SLR QRRAQASYAG PPPTVAELVE AHTNFGFQPD TAPRSPNTGP YPSEQALPIP GTPPPNYDSL RLQPLDVIES DSEGDAI

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Macromolecule #3: Amiloride-sensitive sodium channel subunit gamma

MacromoleculeName: Amiloride-sensitive sodium channel subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.352984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYCLNTNTHG CRRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRRE AESWNSVSEG KQPRFSHRIP L LIFDQDEK ...String:
MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYCLNTNTHG CRRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRRE AESWNSVSEG KQPRFSHRIP L LIFDQDEK GKARDFFTGR KRKVGGSIIH KASNVMHIES KQVVGFQLCS NDTSDCATYT FSSGINAIQE WYKLHYMNIM AQ VPLEKKI NMSYSAEELL VTCFFDGVSC DARNFTLFHH PMHGNCYTFN NRENETILST SMGGSEYGLQ VILYINEEEY NPF LVSSTG AKVIIHRQDE YPFVEDVGTE IETAMVTSIG MHLTESFKLS EPYSQCTEDG SDVPIRNIYN AAYSLQICLH SCFQ TKMVE KCGCAQYSQP LPPAANYCNY QQHPNWMYCY YQLHRAFVQE ELGCQSVCKE ACSFKEWTLT TSLAQWPSVV SEKWL LPVL TWDQGRQVNK KLNKTDLAKL LIFYKDLNQR SIMESPANSI EMLLSNFGGQ LGLWMSCSVV CVIEIIEVFF IDFFSI IAR RQWQKAKEWW AWKQAPPCPE APRSPQGQDN PALDIDDDLP TFNSALHLPP ALGTQVPGTP PPKYNTLRLE RAFSNQL TD TQMLDEL

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Macromolecule #4: 7B1 Fab

MacromoleculeName: 7B1 Fab / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.060393 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(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)(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)(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)(UNK)

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Macromolecule #5: 10D4 Fab

MacromoleculeName: 10D4 Fab / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.805078 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(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)(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)(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 #7: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 7 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK III
Details: 3.5 uL applied, manual blot, fresh 3.5 uL applied, vitrobot blot and freeze.

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252071
FSC plot (resolution estimation)

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