[English] 日本語
Yorodumi
- PDB-8dk6: Structure of hepatitis C virus envelope N-terminal truncated glyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dk6
TitleStructure of hepatitis C virus envelope N-terminal truncated glycoprotein 2 (E2) (residues 456-713) from J6 genotype
Components
  • 2A12 Fab Heavy chain
  • 2A12 Fab light chain
  • Envelope glycoprotein E2
KeywordsVIRAL PROTEIN / Hepatitis C virus glycoprotein 2 (E2)
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHepatitis C virus isolate HC-J6
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKumar, A. / Rohe, T. / Elrod, E.J. / Khan, A.G. / Dearborn, A.D. / Kissinger, R. / Grakoui, A. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2023
Title: Regions of hepatitis C virus E2 required for membrane association.
Authors: Kumar, A. / Rohe, T.C. / Elrod, E.J. / Khan, A.G. / Dearborn, A.D. / Kissinger, R. / Grakoui, A. / Marcotrigiano, J.
History
DepositionJul 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Envelope glycoprotein E2
H: 2A12 Fab Heavy chain
L: 2A12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3424
Polymers76,9183
Non-polymers4241
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.970, 125.540, 157.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Envelope glycoprotein E2


Mass: 29111.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate HC-J6 / Cell (production host): Gnti- HEK293 produced / Cell line (production host): Mammalian cell-line / Production host: Homo sapiens (human) / References: UniProt: A0A2I6PIY1
#2: Antibody 2A12 Fab Heavy chain


Mass: 23462.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hyridoma / Production host: Homo sapiens (human)
#3: Antibody 2A12 Fab light chain


Mass: 24343.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hyridoma / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 8.3, Cryoprotectant used 30% Ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→48.97 Å / Num. obs: 35577 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.062 / Net I/σ(I): 8.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5166 / CC1/2: 0.571 / Rpim(I) all: 0.334 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
iMOSFLM7.0.077data reduction
SCALA7.0.077data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WEB
Resolution: 2.45→48.39 Å / SU ML: 0.2762 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.774 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 3268 5.04 %
Rwork0.2031 61617 -
obs0.2046 35524 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 28 180 4604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284549
X-RAY DIFFRACTIONf_angle_d0.68226221
X-RAY DIFFRACTIONf_chiral_restr0.0446705
X-RAY DIFFRACTIONf_plane_restr0.0051788
X-RAY DIFFRACTIONf_dihedral_angle_d3.25252673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.30881450.28122648X-RAY DIFFRACTION95.13
2.49-2.530.2911430.27612667X-RAY DIFFRACTION94.87
2.53-2.570.33121380.26332776X-RAY DIFFRACTION95.14
2.57-2.610.29941530.26622665X-RAY DIFFRACTION94.91
2.61-2.660.31541380.27072665X-RAY DIFFRACTION94.63
2.66-2.710.27671430.26412721X-RAY DIFFRACTION94.52
2.71-2.770.23021270.25492688X-RAY DIFFRACTION94.78
2.77-2.830.27341390.2452668X-RAY DIFFRACTION95.06
2.83-2.890.25451240.23012760X-RAY DIFFRACTION93.61
2.89-2.960.27721490.22462583X-RAY DIFFRACTION92.8
2.96-3.040.25271330.21162636X-RAY DIFFRACTION91.93
3.04-3.130.26831300.22112696X-RAY DIFFRACTION94.96
3.13-3.230.23311340.222793X-RAY DIFFRACTION96.12
3.23-3.350.2281270.22772685X-RAY DIFFRACTION95.94
3.35-3.480.2921390.21242749X-RAY DIFFRACTION95.03
3.48-3.640.2511340.20042664X-RAY DIFFRACTION94.53
3.64-3.830.26261690.18862668X-RAY DIFFRACTION93.97
3.83-4.070.17091340.17462660X-RAY DIFFRACTION92.98
4.07-4.390.18291120.15862622X-RAY DIFFRACTION91.47
4.39-4.830.15731700.15012627X-RAY DIFFRACTION93.3
4.83-5.530.17751660.15752632X-RAY DIFFRACTION94.24
5.53-6.960.23111780.20762708X-RAY DIFFRACTION95.78
6.96-48.390.23631430.19912636X-RAY DIFFRACTION93.07
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.98701419382-0.6997714499250.3292693286685.32365742061-0.9351463918270.906632118951-0.062851098798-0.1257089014880.07174984499570.07311071960630.234674273582-0.1887602726780.040858795635-0.289915118278-0.1290796963610.263930298285-0.00326931053963-0.0003528727742020.328429928334-0.06201096026950.49458434781846.443-9.46534.33
21.49432900674-2.97221787413-1.005129293835.889834604442.006274130360.988434164245-0.02266484079-0.1658444449380.2389877220210.373713066189-0.04943863972630.6721137782620.192201331059-0.2410409295270.2217060442110.266983985668-0.07843713235280.01483680270550.425275576657-0.05583869308570.67626492587437.892-12.21835.476
33.51172843773-2.31122399102-1.218525140162.471186293740.2136355910791.37457471921-0.08911081255080.07323508141590.1117335502870.09537375203990.189579242353-0.452643343132-0.1410137470550.269742951403-0.07216434961750.301638967342-0.0212638063066-0.03689935734640.372381429742-0.02928550902990.56442594017365.47817.50545.585
40.09107957598370.4734685854190.4687550405592.568595205741.201946345581.464594948290.07515095098490.0602511786219-0.0567880238766-0.06830680694880.0362413966333-0.2472693735220.0708373636704-0.0130828817225-0.1058113432670.244385535015-0.02144380529970.04324823148510.3790032523540.009247077423150.58654676209757.283-0.31931.139
53.54172414591.641419177281.48276716993.075918924411.113135690852.96005387369-0.1943859963570.5697357373060.160968919262-0.628373436910.275507813779-0.15099071751-0.001777070355120.347188525565-0.09187417853820.411889805612-0.01412643151350.1089133305280.338176457791-0.05259419003710.54284231879752.796-12.35318.345
68.027448551022.062436324631.771360477483.570161966434.235673112955.088373296150.3290369088290.4936985444221.248643601260.6105186299050.672216907313-0.105914465034-1.575007632760.211772397601-0.9217112908251.11303689531-0.00523435872583-0.04862410130120.6385927943010.2320723427750.80924343876550.69110.74289.1
72.310028095050.04349192850130.9940754211765.3988237424-3.819266794096.900859309150.15459267152-0.356163262998-0.03665862900140.8431306159380.3432904134770.752102663707-0.710097691196-1.0524113654-0.4479363513690.5655709964110.09767846811040.1190131288450.5531152172410.1134797299610.58439181475240.9044.16785.847
86.27114141373-2.83368047306-0.5331401979769.089625602890.03775814138847.847432566680.180098071546-0.1666796605460.1309266888470.601690254228-0.080765154170.428574706096-0.522590982067-0.727177710572-0.1313867269590.6424156756280.0170298838352-0.02411630426440.357329026060.07536078704880.44110155735248.90810.69782.696
97.97226265862-3.920664267771.758761268617.847537074793.747235094274.84338214177-0.111221758388-0.588930974545-1.397441034140.5842047185780.054527860092-0.669164185025-1.086495894321.047302549580.1163596852860.777841566737-0.0992012792276-0.07862829381730.551364952690.1903467028620.75958149506857.77314.18580.268
106.57215115042-1.786854404973.232656528913.415767955831.673016385055.30595923185-0.143528658039-0.526842248813-0.4686712651090.7644230683330.480383310774-0.120164166901-0.7426776666160.14588630415-0.3384829608920.7973411074110.02441326600180.009754154940760.4397165918550.05430678921550.45713487439151.09820.73575.651
112.284218525810.09020288820820.1440630780514.966914135-0.9784498116536.39647188117-0.352669560478-0.41368318962-0.4846818631921.28423131518-0.01479437538330.902966794755-1.13630829611-0.2271322259940.1818128502280.6849657360780.1203940313260.03231914875590.35401689440.09292094929460.46637153625348.65722.92571.968
121.570474869491.37559325181.331617164411.557854069921.994266826763.05789126166-0.460883976566-0.0511169045628-0.237515130580.6157780515750.464319170819-0.254839252457-0.07262159939450.192876479763-0.1117173908070.5661619052010.0660275025046-0.05307647340710.3247425327150.1153507091180.46769492285753.27520.50268.776
130.9966111210050.6920876217612.868047090173.38825176233-0.116104396539.625592395150.005268895291270.203143141024-0.3518957226270.1567934843610.1848133615990.1581573508340.130841930903-0.2369469719140.0121057987140.169752087177-0.008648613434460.09535313932240.3380628410070.02507898657830.61315674278238.66310.84442.604
142.090699023390.6078232008930.389073122743.187485598430.9990200455835.05802181309-0.0315648467125-0.179264860186-0.1436765162060.1462451537960.05435257361420.153168314801-0.1759967559580.168078799325-0.05267096217320.186358533970.04614369148730.04287560916580.2453585959740.02385063586890.4108427310744.43318.83548.965
156.291356214641.04535506434-0.7412068775695.89284594502-3.303452878585.382112668820.2045524282890.006169599942760.6531864000830.1900854793270.1902653675220.673118544508-0.358548968027-0.135790282015-0.3793843832670.2830494044470.03011440437220.02706979771670.313372948997-0.06652394131380.62179727420837.96421.31747.591
160.2012720922970.0606977568960.1680006714771.662970461760.5447782525980.8719757856220.007334626012390.0758074982261-0.136571295574-0.0549721710174-0.05797550314710.00529100092740.0156484981166-0.02392850411530.04808294618130.193275357055-0.03128615929160.03182531657120.329496879077-0.02368337283870.43471712385744.3822.47636.348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 151:199 )H151 - 199
2X-RAY DIFFRACTION2( CHAIN H AND RESID 200:219 )H200 - 219
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:81 )L1 - 81
4X-RAY DIFFRACTION4( CHAIN L AND RESID 82:155 )L82 - 155
5X-RAY DIFFRACTION5( CHAIN L AND RESID 156:218 )L156 - 218
6X-RAY DIFFRACTION6( CHAIN E AND RESID 491:500 )E491 - 500
7X-RAY DIFFRACTION7( CHAIN E AND RESID 501:540 )E501 - 540
8X-RAY DIFFRACTION8( CHAIN E AND RESID 541:562 )E541 - 562
9X-RAY DIFFRACTION9( CHAIN E AND RESID 563:601 )E563 - 601
10X-RAY DIFFRACTION10( CHAIN E AND RESID 602:617 )E602 - 617
11X-RAY DIFFRACTION11( CHAIN E AND RESID 618:637 )E618 - 637
12X-RAY DIFFRACTION12( CHAIN E AND RESID 638:652 )E638 - 652
13X-RAY DIFFRACTION13( CHAIN H AND RESID 1:17 )H1 - 17
14X-RAY DIFFRACTION14( CHAIN H AND RESID 18:60 )H18 - 60
15X-RAY DIFFRACTION15( CHAIN H AND RESID 61:83 )H61 - 83
16X-RAY DIFFRACTION16( CHAIN H AND RESID 84:150 )H84 - 150

+
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