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- EMDB-44216: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -

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Entry
Database: EMDB / ID: EMD-44216
TitleUbiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP)
Map dataFull map from the gold-standard refinement, globally sharpened using an B-factor of -30 A^2, used for model building and refinement.
Sample
  • Complex: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex)
    • Protein or peptide: Ubiquitin-activating enzyme E1 1
    • Protein or peptide: Polyubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
  • Protein or peptide: Ubiquitin
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 4-aminobutanenitrile
KeywordsUBIQUITIN / E1 / E2 / UBA1 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / LIGASE / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND
Function / homology
Function and homology information


PINK1-PRKN Mediated Mitophagy / Hedgehog ligand biogenesis / Regulation of necroptotic cell death / Josephin domain DUBs / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / RAS processing / Regulation of pyruvate metabolism / Translesion synthesis by REV1 ...PINK1-PRKN Mediated Mitophagy / Hedgehog ligand biogenesis / Regulation of necroptotic cell death / Josephin domain DUBs / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / RAS processing / Regulation of pyruvate metabolism / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / MAPK6/MAPK4 signaling / UCH proteinases / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Formation of Incision Complex in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Aggrephagy / Dual Incision in GG-NER / Pexophagy / Neddylation / Ub-specific processing proteases / Metalloprotease DUBs / Regulation of PTEN localization / Regulation of PTEN stability and activity / nuclear mRNA surveillance of meiosis-specific transcripts / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Formation of TC-NER Pre-Incision Complex / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / SREBP signaling pathway / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / positive regulation of mitotic metaphase/anaphase transition / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin conjugating enzyme activity / enzyme inhibitor activity / meiotic cell cycle / modification-dependent protein catabolic process / protein tag activity / protein polyubiquitination / ubiquitin-protein transferase activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA damage response / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle ...Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-activating enzyme E1 1 / Polyubiquitin / Ubiquitin-ribosomal protein eL40B fusion protein / Ubiquitin-conjugating enzyme E2 4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKochanczyk T / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118080 United States
CitationJournal: Nature / Year: 2024
Title: Structural basis for transthiolation intermediates in the ubiquitin pathway.
Authors: Tomasz Kochańczyk / Zachary S Hann / Michaelyn C Lux / Avelyn Mae V Delos Reyes / Cheng Ji / Derek S Tan / Christopher D Lima /
Abstract: Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin ...Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3 complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
History
DepositionMar 22, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44216.png

Downloads & links

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Map

FileDownload / File: emd_44216.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map from the gold-standard refinement, globally sharpened using an B-factor of -30 A^2, used for model building and refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 408.576 Å		1.06 Å/pix.
x 384 pix.
= 408.576 Å		1.06 Å/pix.
x 384 pix.
= 408.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.535
Minimum - Maximum-1.4838593 - 2.8954902
Average (Standard dev.)0.0003070429 (±0.05424629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 408.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map from the gold-standard refinement (unsharpened).

Fileemd_44216_additional_1.map
AnnotationFull map from the gold-standard refinement (unsharpened).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Full map of 3D class reconstructed using particle...

Fileemd_44216_additional_2.map
AnnotationFull map of 3D class reconstructed using particle alignment information and half-set split from the gold-standard refinement of cluster 5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from the gold-standard refinement.

Fileemd_44216_half_map_1.map
AnnotationHalf map 2 from the gold-standard refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from the gold-standard refinement.

Fileemd_44216_half_map_2.map
AnnotationHalf map 1 from the gold-standard refinement.
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Covalent E1-Ub-E2 transthiolation intermediate mimic complex with...

EntireName: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex)
Components
  • Complex: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex)
    • Protein or peptide: Ubiquitin-activating enzyme E1 1
    • Protein or peptide: Polyubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
  • Protein or peptide: Ubiquitin
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 4-aminobutanenitrile

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Supramolecule #1: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with...

SupramoleculeName: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843

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Macromolecule #1: Ubiquitin-activating enzyme E1 1

MacromoleculeName: Ubiquitin-activating enzyme E1 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 111.764047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE ...String:
SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE PLTGMIASIT DDGVVTMLEE TRHGLENGDF VKFTEVKGMP GLNDGTPRKV EVKGPYTFSI GSVKDLGSAG YN GVFTQVK VPTKISFKSL RESLKDPEYV YPDFGKMMRP PQYHIAFQAL SAFADAHEGS LPRPRNDIDA AEFFEFCKKI AST LQFDVE LDEKLIKEIS YQARGDLVAM SAFLGGAVAQ EVLKATTSKF YPLKQYFYFD SLESLPSSVT ISEETCKPRG CRYD GQIAV FGSEFQEKIA SLSTFLVGAG AIGCEMLKNW AMMGVATGES GHISVTDMDS IEKSNLNRQF LFRPRDVGKL KSECA STAV SIMNPSLTGK ITSYQERVGP ESEGIFGDEF FEKLSLVTNA LDNVEARMYV DRRCVFFEKP LLESGTLGTK GNTQVV VPH LTESYGSSQD PPEKSFPICT LKNFPNRIEH TIAWARDLFE GLFKQPIDNV NMYLSSPNFL ETSLKTSSNP REVLENI RD YLVTEKPLSF EECIMWARLQ FDKFFNNNIQ QLLFNFPKDS VTSTGQPFWS GPKRAPTPLS FDIHNREHFD FIVAAASL Y AFNYGLKSET DPAIYERVLA GYNPPPFAPK SGIKIQVNEN EEAPETAANK DKQELKSIAD SLPPPSSLVG FRLTPAEFE KDDDSNHHID FITAASNLRA MNYDITPADR FKTKFVAGKI VPAMCTSTAV VSGLVCLELV KLVDGKKKIE EYKNGFFNLA IGLFTFSDP IASPKMKVNG KEIDKIWDRY NLPDCTLQEL IDYFQKEEGL EVTMLSSGVS LLYANFQPPK KLAERLPLKI S ELVEQITK KKLEPFRKHL VLEICCDDAN GEDVEVPFIC IKL

UniProtKB: Ubiquitin-activating enzyme E1 1

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Macromolecule #2: Polyubiquitin

MacromoleculeName: Polyubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 8.568769 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin

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Macromolecule #3: Ubiquitin-conjugating enzyme E2 4

MacromoleculeName: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 17.043336 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MALKRINREL ADLGKDPPSS SSAGPVGDDL FHWQATIMGP ADSPYAGGVF FLSIHFPTDY PFKPPKVNFT TRIYHPNINS NGSICLDIL RDQWSPALTI SKVLLSISSL LTDPNPDDPL VPEIAHVYKT DRSRYELSAR EWTRKYAIGG LVPR

UniProtKB: Ubiquitin-conjugating enzyme E2 4

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Macromolecule #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 8.769948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRG

UniProtKB: Ubiquitin-ribosomal protein eL40B fusion protein

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Macromolecule #5: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #6: 4-aminobutanenitrile

MacromoleculeName: 4-aminobutanenitrile / type: ligand / ID: 6 / Number of copies: 1 / Formula: A1AIV
Molecular weightTheoretical: 84.12 Da

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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: 7.2 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% CHAPSO
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 4.0 sec. / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12618
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9b5l:
Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP)

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