[English] 日本語
Yorodumi
- PDB-6gz5: tRNA translocation by the eukaryotic 80S ribosome and the impact ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6gz5
TitletRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)
Components
  • (ribosomal protein ...) x 78
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • E/E-site-tRNA
  • P/P-site-tRNA
  • eukaryotic elongation factor 2 (eEF2)
  • mRNAMessenger RNA
KeywordsRIBOSOME / translocation rabbit ribosome / 80S / eEF2 / head swivel / rotation
Specimen sourceEnterobacteria phage SP6 (bacteriophage)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsFlis, J. / Holm, M. / Rundlet, E.J. / Loerke, J. / Hilal, T. / Dabrowski, M. / Buerger, J. / Mielke, T. / Blanchard, S.C. / Spahn, C.M.T. / Budkevich, T.V.
CitationJournal: Cell Rep / Year: 2018
Title: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Authors: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich
Abstract: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Release: Dec 5, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 5, 2018Structure modelrepositoryInitial release
1.1Dec 19, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0100
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A2: 28S ribosomal RNA
Bv: P/P-site-tRNA
Bx: mRNA
Bw: E/E-site-tRNA
B1: 18S ribosomal RNA
BD: ribosomal protein uS3
BF: ribosomal protein uS7
BK: ribosomal protein eS10
BM: ribosomal protein eS12
BP: ribosomal protein uS19
BQ: ribosomal protein uS9
BR: ribosomal protein eS17
BS: ribosomal protein uS13
BT: ribosomal protein eS19
BU: ribosomal protein uS10
BZ: ribosomal protein eS25
Bc: ribosomal protein eS28
Bd: ribosomal protein uS14
Bf: ribosomal protein eS31
Bg: ribosomal protein RACK 1
BA: ribosomal protein uS2
BB: ribosomal protein eS1
BC: ribosomal protein uS5
BE: ribosomal protein eS4
BG: ribosomal protein eS6
BH: ribosomal protein eS7
BI: ribosomal protein eS8
BJ: ribosomal protein uS4
BL: ribosomal protein uS17
BN: ribosomal protein uS15
BO: ribosomal protein uS11
BV: ribosomal protein eS21
BW: ribosomal protein uS8
BX: ribosomal protein uS12
BY: ribosomal protein eS24
Ba: ribosomal protein eS26
Bb: ribosomal protein eS27
Be: ribosomal protein eS30
A3: 5.8S ribosomal RNA
A4: 5S ribosomal RNA
AA: ribosomal protein uL2
AB: ribosomal protein uL3
AC: ribosomal protein uL4
AD: ribosomal protein uL18
AE: ribosomal protein eL6
AF: ribosomal protein uL30
AG: ribosomal protein eL8
AH: ribosomal protein uL6
AI: ribosomal protein uL16
AJ: ribosomal protein uL5
AL: ribosomal protein eL13
AM: ribosomal protein eL14
AN: ribosomal protein eL15
AO: ribosomal protein uL13
AP: ribosomal protein uL22
AQ: ribosomal protein eL18
AR: ribosomal protein eL19
AS: ribosomal protein eL20
AT: ribosomal protein eL21
AU: ribosomal protein eL22
AV: ribosomal protein uL14
AW: ribosomal protein eL24
AX: ribosomal protein uL23
AY: ribosomal protein uL24
AZ: ribosomal protein eL27
Aa: ribosomal protein uL15
Ab: ribosomal protein eL29
Ac: ribosomal protein eL30
Ad: ribosomal protein eL31
Ae: ribosomal protein eL32
Af: ribosomal protein eL33
Ag: ribosomal protein eL34
Ah: ribosomal protein uL29
Ai: ribosomal protein eL36
Aj: ribosomal protein eL37
Ak: ribosomal protein eL38
Al: ribosomal protein eL39
Am: ribosomal protein eL40
An: ribosomal protein eL41
Ao: ribosomal protein eL42
Ap: ribosomal protein eL43
At: ribosomal protein eL28
Au: ribosomal protein uL1
Aq: ribosomal protein uL11
AK: ribosomal protein uL10
Ct: eukaryotic elongation factor 2 (eEF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,325,455419
Polyers3,316,65886
Non-polymers8,797333
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 7 types, 7 molecules A2BvBxBwB1A3A4

#1: RNA chain 28S ribosomal RNA /


Mass: 1170164.875 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain P/P-site-tRNA


Mass: 24437.535 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: RNA chain mRNA / Messenger RNA


Mass: 3492.122 Da / Num. of mol.: 1
Source: (gene. exp.) Enterobacteria phage SP6 (bacteriophage)
Production host: Enterobacteria phage SP6 (bacteriophage)
#4: RNA chain E/E-site-tRNA


Mass: 24533.586 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#5: RNA chain 18S ribosomal RNA /


Mass: 551108.188 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: RNA chain 5.8S ribosomal RNA /


Mass: 50449.812 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: RNA chain 5S ribosomal RNA /


Mass: 38385.750 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

+
Ribosomal protein ... , 78 types, 78 molecules BDBFBKBMBPBQBRBSBTBUBZBcBdBfBgBABBBCBEBGBHBIBJBLBNBOBVBWBXBY...

#6: Protein/peptide ribosomal protein uS3 /


Mass: 24357.590 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein/peptide ribosomal protein uS7 /


Mass: 21424.836 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#8: Protein/peptide ribosomal protein eS10 /


Mass: 11773.953 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein/peptide ribosomal protein eS12 /


Mass: 13393.658 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein/peptide ribosomal protein uS19 /


Mass: 14273.879 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein/peptide ribosomal protein uS9 /


Mass: 15765.480 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein/peptide ribosomal protein eS17 /


Mass: 14447.793 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein/peptide ribosomal protein uS13 /


Mass: 16383.064 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein/peptide ribosomal protein eS19 /


Mass: 15822.219 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein/peptide ribosomal protein uS10 /


Mass: 11029.072 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein/peptide ribosomal protein eS25 /


Mass: 9801.748 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein/peptide ribosomal protein eS28 /


Mass: 7007.069 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein/peptide ribosomal protein uS14 /


Mass: 6121.210 Da / Num. of mol.: 1
Source: (gene. exp.) Enterobacteria phage SP6 (bacteriophage)
Production host: Enterobacteria phage SP6 (bacteriophage)
#19: Protein/peptide ribosomal protein eS31 /


Mass: 8645.277 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein/peptide ribosomal protein RACK 1 / Ribosome


Mass: 34726.164 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein/peptide ribosomal protein uS2 /


Mass: 24245.740 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein/peptide ribosomal protein eS1 /


Mass: 24660.012 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein/peptide ribosomal protein uS5 /


Mass: 24574.971 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein/peptide ribosomal protein eS4 /


Mass: 28893.043 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein/peptide ribosomal protein eS6 /


Mass: 26913.867 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein/peptide ribosomal protein eS7 /


Mass: 20990.465 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein/peptide ribosomal protein eS8 /


Mass: 24132.191 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein/peptide ribosomal protein uS4 /


Mass: 21222.221 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein/peptide ribosomal protein uS17 /


Mass: 17910.176 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein/peptide ribosomal protein uS15 /


Mass: 17057.113 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein/peptide ribosomal protein uS11 /


Mass: 14544.659 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein/peptide ribosomal protein eS21 /


Mass: 8863.111 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: Protein/peptide ribosomal protein uS8 /


Mass: 14734.357 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein/peptide ribosomal protein uS12 /


Mass: 15626.392 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: Protein/peptide ribosomal protein eS24 /


Mass: 14489.176 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein/peptide ribosomal protein eS26 /


Mass: 11087.117 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein/peptide ribosomal protein eS27 /


Mass: 9000.570 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein/peptide ribosomal protein eS30 /


Mass: 6239.447 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein/peptide ribosomal protein uL2 /


Mass: 27456.158 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein/peptide ribosomal protein uL3 /


Mass: 45222.949 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide ribosomal protein uL4 /


Mass: 41171.547 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein/peptide ribosomal protein uL18 /


Mass: 34091.371 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein/peptide ribosomal protein eL6 /


Mass: 22262.428 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein/peptide ribosomal protein uL30 /


Mass: 27733.146 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein/peptide ribosomal protein eL8 /


Mass: 26724.568 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein/peptide ribosomal protein uL6 /


Mass: 21770.355 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein/peptide ribosomal protein uL16 /


Mass: 24150.484 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein/peptide ribosomal protein uL5 /


Mass: 19270.318 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein/peptide ribosomal protein eL13 /


Mass: 23574.697 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein/peptide ribosomal protein eL14 /


Mass: 16220.309 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein/peptide ribosomal protein eL15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein/peptide ribosomal protein uL13 /


Mass: 22820.395 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein/peptide ribosomal protein uL22 /


Mass: 17757.627 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein/peptide ribosomal protein eL18 /


Mass: 21556.482 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein/peptide ribosomal protein eL19 /


Mass: 21742.146 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#58: Protein/peptide ribosomal protein eL20 /


Mass: 20661.340 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein/peptide ribosomal protein eL21 /


Mass: 18276.518 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#60: Protein/peptide ribosomal protein eL22 /


Mass: 11481.248 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#61: Protein/peptide ribosomal protein uL14 /


Mass: 13828.295 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein/peptide ribosomal protein eL24 /


Mass: 14087.417 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein/peptide ribosomal protein uL23 /


Mass: 13614.023 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein/peptide ribosomal protein uL24 /


Mass: 15161.899 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#65: Protein/peptide ribosomal protein eL27 /


Mass: 15647.584 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#66: Protein/peptide ribosomal protein uL15 /


Mass: 16473.340 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: Protein/peptide ribosomal protein eL29 /


Mass: 7996.388 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein/peptide ribosomal protein eL30 /


Mass: 11500.556 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein/peptide ribosomal protein eL31 /


Mass: 12506.581 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#70: Protein/peptide ribosomal protein eL32 /


Mass: 15179.215 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#71: Protein/peptide ribosomal protein eL33 /


Mass: 12433.548 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein/peptide ribosomal protein eL34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein/peptide ribosomal protein uL29 /


Mass: 14462.429 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein/peptide ribosomal protein eL36 /


Mass: 11373.708 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein/peptide ribosomal protein eL37 /


Mass: 9864.596 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein/peptide ribosomal protein eL38 /


Mass: 8107.752 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein/peptide ribosomal protein eL39 /


Mass: 6295.562 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein/peptide ribosomal protein eL40 /


Mass: 5957.237 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: Protein/peptide ribosomal protein eL41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: Protein/peptide ribosomal protein eL42 /


Mass: 12345.776 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: Protein/peptide ribosomal protein eL43 /


Mass: 10168.153 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: Protein/peptide ribosomal protein eL28 /


Mass: 13991.366 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: Protein/peptide ribosomal protein uL1 /


Mass: 24879.422 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein/peptide ribosomal protein uL11 /


Mass: 16290.794 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: Protein/peptide ribosomal protein uL10 /


Mass: 22217.840 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

-
Protein/peptide , 1 types, 1 molecules Ct

#86: Protein/peptide eukaryotic elongation factor 2 (eEF2)


Mass: 95056.734 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

-
Non-polymers , 3 types, 333 molecules

#87: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 327 / Formula: Mg / Magnesium
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn / Zinc
#89: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Formula: C10H17N6O13P3
Comment: GppNHp (GMPPNP, energy-carrying molecule analogue) *YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1translocation intermediate TI-POST-3RIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 860MULTIPLE SOURCES
2translocation intermediate TI-POST-3RIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 861NATURAL
3translocation intermediate TI-POST-3COMPLEX3,181RECOMBINANT
4translocation intermediate TI-POST-3COMPLEX41NATURAL
Molecular weightValue: 4.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229986Oryctolagus cuniculus (rabbit)
33194966Enterobacteria phage SP6 (bacteriophage)
444932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Enterobacteria phage SP6 (bacteriophage)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 5 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 270000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 44522 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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