[English] 日本語
Yorodumi
- PDB-5j5o: Translation initiation factor 4E in complex with m7GppppG mRNA 5'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j5o
TitleTranslation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / m7GppppG / mRNA 5' cap analog
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / postsynapse / DNA-binding transcription factor binding / nuclear body / negative regulation of translation / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6G0 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.867 Å
AuthorsWarminski, M. / Nowak, E. / Rydzik, A.M. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationDI2012 024842 Poland
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.
Authors: Rydzik, A.M. / Warminski, M. / Sikorski, P.J. / Baranowski, M.R. / Walczak, S. / Kowalska, J. / Zuberek, J. / Lukaszewicz, M. / Nowak, E. / W Claridge, T.D. / Darzynkiewicz, E. / Nowotny, M. / Jemielity, J.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,23710
Polymers88,5804
Non-polymers2,6576
Water6,359353
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8553
Polymers22,1451
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8553
Polymers22,1451
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7632
Polymers22,1451
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7632
Polymers22,1451
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.990, 38.030, 146.640
Angle α, β, γ (deg.)88.55, 84.70, 76.67
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Eukaryotic translation initiation factor 4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22145.113 Da / Num. of mol.: 4 / Fragment: UNP residues 28-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical
ChemComp-6G0 / 5'-O-[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]-7-methylguanosine


Mass: 618.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H20N5O17P4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 % / Description: Thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 13% PEG5000MME, 0.1M Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.867→36.82 Å / Num. obs: 60259 / % possible obs: 91.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.5
Reflection shellResolution: 1.867→1.92 Å / Rmerge(I) obs: 0.555

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 1.867→36.82 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2634 2234 3.71 %
Rwork0.2208 --
obs0.2223 60257 91.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.867→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 160 353 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086212
X-RAY DIFFRACTIONf_angle_d1.0318502
X-RAY DIFFRACTIONf_dihedral_angle_d18.2273645
X-RAY DIFFRACTIONf_chiral_restr0.056902
X-RAY DIFFRACTIONf_plane_restr0.0061063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8673-1.90790.37141140.29132960X-RAY DIFFRACTION74
1.9079-1.95220.32241200.26353120X-RAY DIFFRACTION80
1.9522-2.00110.27711260.24933272X-RAY DIFFRACTION80
2.0011-2.05520.28091250.24063250X-RAY DIFFRACTION83
2.0552-2.11560.28071350.23583492X-RAY DIFFRACTION87
2.1156-2.18390.25591340.23993491X-RAY DIFFRACTION90
2.1839-2.2620.32561410.23653649X-RAY DIFFRACTION91
2.262-2.35250.31861440.22773747X-RAY DIFFRACTION94
2.3525-2.45960.27631440.23973753X-RAY DIFFRACTION96
2.4596-2.58920.29451470.22943824X-RAY DIFFRACTION96
2.5892-2.75140.26261530.23043975X-RAY DIFFRACTION99
2.7514-2.96370.27191520.22173927X-RAY DIFFRACTION99
2.9637-3.26180.27361480.21223850X-RAY DIFFRACTION98
3.2618-3.73340.23921510.1983930X-RAY DIFFRACTION98
3.7334-4.70220.21741510.19513937X-RAY DIFFRACTION98
4.7022-36.82680.23861490.21713846X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.12662.89870.47816.31771.73443.07880.2426-0.103-0.20960.4188-0.0279-0.78230.08980.3069-0.24390.1534-0.06830.00160.0798-0.04370.4548-44.615678.3776-4.3929
24.3195-1.13880.53260.4146-0.32940.46250.133-0.0595-0.3959-0.02880.01560.1966-0.0438-0.1344-0.11080.18470.02080.00770.0637-0.02090.2454-72.680770.1535-11.1414
34.7290.72490.77782.3157-0.16930.55440.0305-0.0580.49710.1158-0.01920.01790.1146-0.0095-0.0140.1790.0091-0.0020.0805-0.04440.1982-59.359772.1714-5.246
41.1325-0.46570.37582.2787-0.27481.6331-0.06610.0745-0.0187-0.12110.0473-0.09640.0429-0.00750.01510.1293-0.00560.02340.0712-0.0390.175-60.538966.3919-16.8855
51.90871.0434-0.69064.3682-1.4322.1568-0.08840.2048-0.0305-0.36480.09090.02950.1607-0.0764-0.05630.1759-0.03070.02570.0906-0.07830.1831-63.45166.3836-23.4481
62.6308-0.99360.7412.6454-0.76641.50480.1780.3839-0.0119-0.4437-0.1099-0.19730.0750.3471-0.03930.2233-0.00340.17250.1775-0.09680.2273-50.8765.0779-27.3197
71.4169-1.9668-0.73152.9620.51472.48350.35730.5417-0.4032-0.7887-0.26540.12190.0641-0.0455-0.0760.34810.0110.01950.2118-0.09910.2208-61.393662.9217-30.4491
85.12562.3175-2.76932.7205-2.44837.2410.20060.26170.74630.07780.0570.1356-0.65330.17-0.30730.1275-0.05240.0830.26870.08010.3889-29.609363.1025-64.1972
91.71832.9877-0.2255.8613-0.80290.28770.02310.0036-0.2256-0.06110.0674-0.0937-0.0191-0.008-0.02240.09080.03110.07690.1931-0.0440.2639-44.150737.0931-57.3404
101.9523-0.2845-0.55781.3178-0.92213.03190.04220.134-0.1202-0.0599-0.0811-0.01790.16670.11590.01530.08610.01520.05760.0834-0.03580.1777-41.060547.5997-57.6331
113.5531-0.42691.60380.2881-0.36970.8558-0.01390.1661-0.1690.0877-0.02330.36310.07-0.0130.04320.14410.01390.08160.1908-0.11210.3235-56.856151.5426-49.6876
122.7168-1.8638-0.36832.2327-1.10581.9961-0.0049-0.11270.18450.1937-0.0587-0.098-0.19780.13110.04110.09430.01890.07920.0792-0.06650.2002-42.696156.4384-51.0014
138.71221.58382.82391.68251.22893.15140.0792-0.6804-0.11330.1426-0.10150.02660.2128-0.22630.0170.0981-0.00820.11460.14210.01380.213-46.443247.4403-45.4343
140.9908-0.6853-0.05861.4514-0.47052.9652-0.1628-0.29180.13780.35060.15260.0291-0.3651-0.0704-0.06170.21040.02780.08690.1946-0.13630.1896-44.587360.3171-41.8094
151.9996-1.4512-0.85273.06590.20083.709-0.2848-0.3563-0.18470.43220.21920.31840.2777-0.11540.07160.27760.04640.13080.2439-0.06870.1876-49.398850.9589-38.4198
160.3286-1.47620.80426.7566-4.2765.1792-0.0014-0.1384-0.1344-0.37140.47230.1514-0.0013-0.6664-0.38580.4781-0.10880.03740.2092-0.02840.1422-63.684763.25836.8962
170.73931.3507-0.02112.6006-0.70873.44110.03930.0448-0.43570.3716-0.0886-1.08530.53940.5256-0.02420.59210.0059-0.3010.2062-0.00130.7386-43.676646.396311.7815
180.14440.18140.10990.9001-0.16210.25450.2209-0.1875-0.11030.731-0.1575-0.37950.12130.0685-0.06020.7341-0.1299-0.23780.13070.01220.3847-55.639645.318915.294
192.30271.43041.85621.21010.83153.1281-0.0071-0.3860.32130.121-0.26240.0873-0.4325-0.33810.46570.72-0.1339-0.35570.2950.00640.3816-57.061652.240722.8611
201.6760.99970.86990.68610.51580.45350.0564-0.35360.28620.7855-0.24230.0188-0.1086-0.09570.16061.0117-0.2545-0.16940.30020.05080.2954-58.474247.020526.4732
210.6629-0.60021.1081.9632-0.95637.07990.5709-0.3738-0.609-0.2455-0.21930.29091.8439-0.8041-0.37261.2885-0.2337-0.26240.81960.13310.4361-61.766740.601730.0835
221.4245-0.72380.06210.3671-0.03180.0026-0.1678-0.9412-0.35330.19330.37470.1315-0.0195-0.5136-0.17341.1734-0.2273-0.39290.8630.25970.6038-52.302243.776933.8797
235.61170.8122-0.32014.6211-4.70248.6862-0.06080.0395-0.1495-0.4755-0.3142-0.350.88510.33020.37730.15930.07050.06450.4134-0.0820.1874-49.085347.8015-75.0018
242.4424-0.02150.62260.1641-0.50371.6730.07250.65371.3895-0.0932-0.021-0.0518-0.4732-0.2862-0.02230.25970.05820.02340.6290.3530.8555-63.06372.6324-81.2567
253.5758-0.76790.30440.56730.33841.45310.01640.51970.8219-0.0397-0.03940.0169-0.18590.0023-0.01650.11670.02880.05570.40740.05820.3193-58.368860.5155-75.4365
265.5164-0.00091.30810.7302-1.08052.17210.07060.42830.665-0.06340.15990.231-0.2513-0.4021-0.25910.12080.05030.07660.50470.18320.3874-72.526964.634-76.4002
272.63020.2685-1.16270.0282-0.09940.93680.01910.39880.3417-0.08890.0244-0.0637-0.1016-0.0445-0.10240.14260.00690.08320.71930.29840.419-57.252966.6455-85.9557
282.87120.57050.27210.8337-0.2690.3076-0.04540.92930.2995-0.2044-0.01130.0526-0.061-0.04140.01250.17680.0113-0.00820.90750.05950.2807-67.2957.4094-87.8413
294.59770.0765-1.8532.1121-0.78952.6878-0.19440.7124-0.0873-0.318-0.0407-0.28110.32170.32650.42780.27180.02770.06980.96520.26990.3624-58.387957.3105-91.3968
302.3409-1.2842-0.53954.10920.67121.92820.19880.53250.2018-0.3980.0325-0.2223-0.1476-0.0652-0.24980.27650.03650.03891.04390.2560.3167-64.249262.6358-93.9521
310.3997-0.2029-0.80231.52510.13181.6627-0.190.3613-0.1733-0.6038-0.0174-0.30440.2044-0.32330.18840.4052-0.05190.10541.2049-0.02030.3394-62.633650.6217-96.9335
321.6379-0.63350.97011.1143-1.97697.392-0.2397-0.12390.1647-0.64860.430.60760.6218-1.3736-0.23110.64040.1542-0.05391.52080.2790.4871-71.932254.102-98.0836
330.0354-0.04310.02070.0527-0.02440.0111-0.32780.44880.3958-1.25410.36651.3314-0.0468-0.5186-0.01850.6509-0.0828-0.23391.45730.31260.7028-66.002964.1422-103.0068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 172 )
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 187 )
7X-RAY DIFFRACTION7chain 'A' and (resid 188 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 110 )
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 125 )
12X-RAY DIFFRACTION12chain 'B' and (resid 126 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 172 )
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 187 )
15X-RAY DIFFRACTION15chain 'B' and (resid 188 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 31 through 42 )
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 66 )
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 142 )
19X-RAY DIFFRACTION19chain 'C' and (resid 143 through 156 )
20X-RAY DIFFRACTION20chain 'C' and (resid 157 through 187 )
21X-RAY DIFFRACTION21chain 'C' and (resid 188 through 199 )
22X-RAY DIFFRACTION22chain 'C' and (resid 200 through 217 )
23X-RAY DIFFRACTION23chain 'D' and (resid 31 through 42 )
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 56 )
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 78 )
26X-RAY DIFFRACTION26chain 'D' and (resid 79 through 88 )
27X-RAY DIFFRACTION27chain 'D' and (resid 89 through 104 )
28X-RAY DIFFRACTION28chain 'D' and (resid 105 through 142 )
29X-RAY DIFFRACTION29chain 'D' and (resid 143 through 156 )
30X-RAY DIFFRACTION30chain 'D' and (resid 157 through 172 )
31X-RAY DIFFRACTION31chain 'D' and (resid 173 through 187 )
32X-RAY DIFFRACTION32chain 'D' and (resid 188 through 199 )
33X-RAY DIFFRACTION33chain 'D' and (resid 200 through 217 )

+
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://pdbjlvh1.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