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- EMDB-3019: Structure of HCV IRES bound to the human ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3019
TitleStructure of HCV IRES bound to the human ribosome
Map dataReconstruction of hepatitis C virus IRES bound to human ribosome
Sample
  • Sample: Hepatitis C virus IRES bound to human ribosome
  • Complex: 40S ribosome
  • RNA: Hepatitis-C virus IRES
KeywordsHuman ribosome / IRES / Hepatitis C virus / translation initiation
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / supercoiled DNA binding / activation-induced cell death of T cells / neural crest cell differentiation / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / exit from mitosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / optic nerve development / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / retinal ganglion cell axon guidance / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / erythrocyte development / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / spindle assembly / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of intrinsic apoptotic signaling pathway / rough endoplasmic reticulum / laminin binding / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of cell cycle / translation initiation factor binding / signaling adaptor activity / gastrulation / Maturation of protein E / Maturation of protein E / MDM2/MDM4 family protein binding / positive regulation of microtubule polymerization / cytosolic ribosome
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / 60S ribosomal protein L19 / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e
Similarity search - Domain/homology
Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 ...Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesHomo sapiens (human) / Hepatitis C virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsQuade N / Leibundgut M / Boehringer D / van den Heuvel J / Ban N
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution.
Authors: Nick Quade / Daniel Boehringer / Marc Leibundgut / Joop van den Heuvel / Nenad Ban /
Abstract: Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation ...Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.
History
DepositionMay 20, 2015-
Header (metadata) releaseJul 1, 2015-
Map releaseJul 15, 2015-
UpdateAug 12, 2015-
Current statusAug 12, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a2q
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3019.png

Downloads & links

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Map

FileDownload / File: emd_3019.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of hepatitis C virus IRES bound to human ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.25578699 - 0.47499382
Average (Standard dev.)0.00376542 (±0.02093141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z300.240300.240300.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.2560.4750.004

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Supplemental data

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Sample components

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Entire : Hepatitis C virus IRES bound to human ribosome

EntireName: Hepatitis C virus IRES bound to human ribosome
Components
  • Sample: Hepatitis C virus IRES bound to human ribosome
  • Complex: 40S ribosome
  • RNA: Hepatitis-C virus IRES

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Supramolecule #1000: Hepatitis C virus IRES bound to human ribosome

SupramoleculeName: Hepatitis C virus IRES bound to human ribosome / type: sample / ID: 1000 / Oligomeric state: IRES bound to ribosome / Number unique components: 2
Molecular weightTheoretical: 1.45 MDa

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Supramolecule #1: 40S ribosome

SupramoleculeName: 40S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S
Ref GO0: GO:0005840
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HEK293-6E / Location in cell: Cytosole
Molecular weightTheoretical: 1.35 MDa

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Macromolecule #1: Hepatitis-C virus IRES

MacromoleculeName: Hepatitis-C virus IRES / type: rna / ID: 1 / Name.synonym: HCV IRES / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Hepatitis C virus
Molecular weightTheoretical: 100 KDa
SequenceString: CTCCCCTGTG AGGAACTACT GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GCCTCCAGGA CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GGAATTGCCA GGACGACCGG GTCCTTTCTT GGATAAACCC ...String:
CTCCCCTGTG AGGAACTACT GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GCCTCCAGGA CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GGAATTGCCA GGACGACCGG GTCCTTTCTT GGATAAACCC GCTCAATGCC TGGAGATTTG GGCGTGCCCC CGCAAGACTG CTAGCCGAGT AGTGTTGGGT CGCGAAAGGC CTTGTGGTAC TGCCTGATAG GGTGCTTGCG AGTGCCCCGG GAGGTCTCGT AGACCGTGCA CCATGAGCAC AAATC

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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

Concentration0.4 mg/mL
BufferpH: 7.6 / Details: 20mM HEPES, 100 mM KCl, 5 mM MgCl2
GridDetails: 200 mesh Quantifoil R 2/2 holey carbon grids with a thin continuous carbon support film applied
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 80 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateNov 20, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20 e/Å2
Details: movie mode readout in FEI EPU: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: per detector frame
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 404357

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Atomic model buiding 1

Initial modelPDB ID:

4w23
PDB Unreleased entry

SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and O (proteins) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 2

Initial modelPDB ID:

4upy
PDB Unreleased entry


Chain - Chain ID: C
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 3

Initial modelPDB ID:

1p5p


Chain - Chain ID: A
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 4

Initial modelPDB ID:

1idv


Chain - Chain ID: A
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 5

Initial modelPDB ID:

1kh6


Chain - Chain ID: A
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 6

Initial modelPDB ID:

1f84


Chain - Chain ID: A
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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Atomic model buiding 7

Initial modelPDB ID:

3t4b


Chain - Chain ID: A
SoftwareName: Chimera
DetailsThe coordinate model of the 40S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and refined using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a2q:
Structure of the HCV IRES bound to the human ribosome

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