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- EMDB-3495: Structure of the 30S Pre-Initiation Complex 2 (30S IC-2) Stalled ... -

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Entry
Database: EMDB / ID: 3495
TitleStructure of the 30S Pre-Initiation Complex 2 (30S IC-2) Stalled by GE81112
Map data
Sample30S Pre-Initiation Complex IC-2 Stalled by GE81112
  • (nucleic-acidNucleic acid) x 2
  • (30S ribosomal protein ...) x 20
  • (Translation initiation factor IF- ...) x 4
  • ligand
Function / homologyRibosomal protein S16, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S9, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S4/S9 / Ribosomal protein S14, bacterial/plastid ...Ribosomal protein S16, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S9, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S4/S9 / Ribosomal protein S14, bacterial/plastid / 30S ribosomal protein S17 / Translation initiation factor IF- 2, domain 3 / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S11, bacterial-type / Ribosomal protein S8 superfamily / Ribosomal protein S10, conserved site / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Translation initiation factor IF- 2 / K homology domain-like, alpha/beta / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S3, conserved site / Translation initiation factor 3, conserved site / Translation initiation factor 3, N-terminal / Translation initiation factor 3, C-terminal / Ribosomal protein S17, conserved site / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Initiation factor 2 associated domain, bacterial / Translation initiation factor 1A / IF-1 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Translation initiation factor IF-3, C-terminal domain / Ribosomal protein S16 / Ribosomal protein S18 / Ribosomal protein S21 / Ribosomal protein S6 / Ribosomal protein S17 / S4 domain / Ribosomal protein S20 / Ribosomal protein S5, C-terminal domain / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-3, N-terminal domain / KH domain / Bacterial translation initiation factor IF-2 associated region / Translation-initiation factor 2 / Ribosomal protein S9/S16 / Ribosomal protein S10p/S20e / Ribosomal protein S20 superfamily / Ribosomal protein S21 superfamily / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Translation initiation factor IF-2, domain 3 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Elongation factor Tu GTP binding domain / Ribosomal protein S5, N-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S5, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein S8 signature. / Ribosomal protein S12 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Translation initiation factor aIF-2, bacterial-like / Ribosomal protein S3 signature. / Ribosomal protein S13-like, H2TH / Ribosomal protein S17/S11 / Ribosomal protein S16 / Ribosomal protein S6
Function and homology information
SourceEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Geobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / 13.5 Å resolution
AuthorsLopez-Alonso JP / Fabbretti A / Kaminishi T / Iturrioz I / Brandi L / Gil Carton D / Gualerzi C / Fucini P / Connell S
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.
Authors: Jorge P López-Alonso / Attilio Fabbretti / Tatsuya Kaminishi / Idoia Iturrioz / Letizia Brandi / David Gil-Carton / Claudio O Gualerzi / Paola Fucini / Sean R Connell
Abstract: In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the ...In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.
Validation ReportPDB-ID: 5me1

SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0895
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0895
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  • Surface view with fitted model
  • Atomic models: : PDB-5me1
  • Surface level: 0.0895
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3495.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
2.02 Å/pix.
= 363.6 Å
180 pix
2.02 Å/pix.
= 363.6 Å
180 pix
2.02 Å/pix.
= 363.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density
Contour Level:0.0895 (by author), 0.0895 (movie #1):
Minimum - Maximum-0.06792107 - 0.3809387
Average (Standard dev.)0.0056579066 (0.031846266)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin0.00.00.0
Limit179.0179.0179.0
Spacing180180180
CellA=B=C: 363.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z363.600363.600363.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0680.3810.006

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Supplemental data

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Mask #1

Fileemd_3495_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire 30S Pre-Initiation Complex IC-2 Stalled by GE81112

EntireName: 30S Pre-Initiation Complex IC-2 Stalled by GE81112 / Number of components: 28

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Component #1: protein, 30S Pre-Initiation Complex IC-2 Stalled by GE81112

ProteinName: 30S Pre-Initiation Complex IC-2 Stalled by GE81112 / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Details: Taken from PDB entry 4YBB / Structure: OTHER / Synthetic: No
Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCC(G7M)CGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUCA
MassTheoretical: 497.404969 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.211058 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.637445 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.683053 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.464126 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Details: Taken from PDB entry 4YBB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #23: protein, Translation initiation factor IF-1

ProteinName: Translation initiation factor IF-1 / Details: Taken from PDB entry 1HR0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.247664 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #24: protein, Translation initiation factor IF-2

ProteinName: Translation initiation factor IF-2 / Details: Taken from PDB entry 3JCN / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 97.498164 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #25: protein, Translation initiation factor IF-3

ProteinName: Translation initiation factor IF-3 / Details: Taken from PDB entry 1TIF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.717984 kDa
SourceSpecies: Geobacillus stearothermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #26: protein, Translation initiation factor IF-3

ProteinName: Translation initiation factor IF-3 / Details: Taken from PDB entry 2IFE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.667477 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #27: nucleic-acid, fMet-tRNA

Nucleic-acidName: fMet-tRNA / Class: RNA / Details: Taken from PDB entry 3JCN / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGG(4SU)GG AGCAGCCUGG (H2U)AGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.818893 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #28: ligand, N-FORMYLMETHIONINE

LigandName: N-FORMYLMETHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.177221 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.7
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000.0 X (nominal), 74183.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 261

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 26776
3D reconstructionSoftware: RELION / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Details: The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the volume, the conformation of the linking bases was not minimized. In addition, some of the clashes of the model are produced by flexible loops or protein side chains that were not refined.
Input PDB model: 4YBB, 3JCN, 3JCN, 1HR0, 2IFE, 1TIF
Chain ID: b, v, W, A, A
Output model

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