[English] 日本語
Yorodumi
- PDB-4v6w: Structure of the D. melanogaster 80S ribosome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4v6w
TitleStructure of the D. melanogaster 80S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 44
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 2S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • E-tRNA
  • Elongation factor 2EEF2
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Vig2, isoform B
KeywordsRIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry
Function / homologyElongation Factor G, domain II / Plectin/S10 domain / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / Ribosomal protein L14 / Elongation factor Tu domain 2 / S25 ribosomal protein / Ribosomal protein S5, C-terminal domain / Ribosomal L28e protein family ...Elongation Factor G, domain II / Plectin/S10 domain / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / Ribosomal protein L14 / Elongation factor Tu domain 2 / S25 ribosomal protein / Ribosomal protein S5, C-terminal domain / Ribosomal L28e protein family / Elongation factor G, domain IV / Ribosomal protein L6, N-terminal domain / Ribosomal protein L23, N-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein S30 / Hyaluronan / mRNA binding family / Ribosomal L29e protein family / Ribosomal L27e protein family / KH domain / Ribosomal protein L19e / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal L22e protein family / Ribosomal protein S26e / Ribosomal protein L13e / S4 domain / Ribosomal protein S27a / Ribosomal protein L32 / Ribosomal protein S27 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L41 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L31e / Ribosomal protein L3 signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L15 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L19e signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S3 signature. / Ribosomal protein S6e signature. / Ribosomal protein L29 signature. / Ribosomal protein S19 signature. / Ubiquitin domain signature. / RS4NT (NUC023) domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal L30 N-terminal domain / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein SA C-terminus / Ribosomal_S17 N-terminal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein S17 signature. / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein L34e / Ribosomal protein L6e / Ribosomal protein S5 signature. / Ribosomal protein L21 superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L11, C-terminal domain superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Elongation factor Tu GTP binding domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S19
Function and homology information
Specimen sourceDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6 Å resolution
AuthorsAnger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R.
CitationJournal: Nature / Year: 2013
Title: Structures of the human and Drosophila 80S ribosome.
Authors: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann
Abstract: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 27, 2013 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 8, 2015Structure modelOther

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5591
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Az: Elongation factor 2
Ag: Guanine nucleotide-binding protein subunit beta-like protein
AU: 40S ribosomal protein S20
AK: 40S ribosomal protein S10a
AO: 40S ribosomal protein S14
AX: 40S ribosomal protein S23
AM: 40S ribosomal protein S12
AS: 40S ribosomal protein S18
Ad: 40S ribosomal protein S29
AN: 40S ribosomal protein S13
AL: 40S ribosomal protein S11
AR: 40S ribosomal protein S17
AP: 40S ribosomal protein S15, isoform A
AT: 40S ribosomal protein S19a
AB: 40S ribosomal protein S3a
AA: 40S ribosomal protein SA
AV: 40S ribosomal protein S21
AY: 40S ribosomal protein S24
AZ: 40S ribosomal protein S25
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
Ac: 40S ribosomal protein S28
AD: 40S ribosomal protein S3
Ae: 40S ribosomal protein S30, isoform A
Af: 40S ribosomal protein S27a
AJ: 40S ribosomal protein S9
AE: 40S ribosomal protein S4
AC: 40S ribosomal protein S2
AG: 40S ribosomal protein S6
AF: 40S ribosomal protein S5a
AH: 40S ribosomal protein S7
AW: 40S ribosomal protein S15Aa
AI: 40S ribosomal protein S8
AQ: 40S ribosomal protein S16
Ah: Vig2, isoform B
B2: 18S ribosomal RNA
BC: E-tRNA
Cz: 60S ribosomal protein L10a-2
Cq: 60S acidic ribosomal protein P0
CK: 60S ribosomal protein L12
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: 60S ribosomal protein L23
CM: 60S ribosomal protein L14
Ca: 60S ribosomal protein L27a
CN: 60S ribosomal protein L15
CI: 60S ribosomal protein L10
CD: 60S ribosomal protein L5
CQ: 60S ribosomal protein L18
CR: 60S ribosomal protein L19
CA: 60S ribosomal protein L8
CS: 60S ribosomal protein L18a
CT: 60S ribosomal protein L21
CP: 60S ribosomal protein L17
CU: 60S ribosomal protein L22
CX: 60S ribosomal protein L23A
CY: 60S ribosomal protein L26
CW: 60S ribosomal protein L24
CZ: 60S ribosomal protein L27
Cr: 60S ribosomal protein L28
Ch: 60S ribosomal protein L35
Cb: 60S ribosomal protein L29
CB: 60S ribosomal protein L3
CF: 60S ribosomal protein L7
Cc: 60S ribosomal protein L30
Cd: 60S ribosomal protein L31
Ce: 60S ribosomal protein L32
Cf: 60S ribosomal protein L35A
Cg: 60S ribosomal protein L34a
Ci: 60S ribosomal protein L36
Cj: 60S ribosomal protein L37-A
Ck: 60S ribosomal protein L38
Cl: 60S ribosomal protein L39
CC: 60S ribosomal protein L4
Cm: 60S ribosomal protein L40
Cn: 60S ribosomal protein L41
Cp: 60S ribosomal protein L37a
Co: 60S ribosomal protein L36A
CJ: 60S ribosomal protein L11
CH: 60S ribosomal protein L9
CE: 60S ribosomal protein L6, isoform A
CG: 60S ribosomal protein L7a
A5: 28S ribosomal RNA
A9: 2S ribosomal RNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)3,670,25086
Polyers3,670,25086
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein/peptide , 4 types, 4 molecules AzAgAhCq

#1: Protein/peptide Elongation factor 2 / EEF2 / EF-2


Mass: 94585.961 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P13060
#2: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor of activated protein kinase C homolog


Mass: 35661.934 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O18640
#35: Protein/peptide Vig2, isoform B


Mass: 13542.481 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VBX3
#39: Protein/peptide 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E


Mass: 24401.459 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source: (natural) Drosophila melanogaster (fruit fly)

+
40S ribosomal protein ... , 32 types, 32 molecules AUAKAOAXAMASAdANALARAPATABAAAVAYAZAaAbAcADAeAfAJAEACAGAFAHAWAIAQ

#3: Protein/peptide 40S ribosomal protein S20 /


Mass: 13513.744 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P55828
#4: Protein/peptide 40S ribosomal protein S10a /


Mass: 18259.645 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VB14
#5: Protein/peptide 40S ribosomal protein S14 /


Mass: 16294.790 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P14130, UniProt:C0HKA0*PLUS
#6: Protein/peptide 40S ribosomal protein S23 /


Mass: 16054.750 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q8T3U2
#7: Protein/peptide 40S ribosomal protein S12 /


Mass: 15191.617 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P80455
#8: Protein/peptide 40S ribosomal protein S18 /


Mass: 17649.631 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P41094
#9: Protein/peptide 40S ribosomal protein S29 /


Mass: 6603.676 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VH69
#10: Protein/peptide 40S ribosomal protein S13 /


Mass: 17216.436 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q03334
#11: Protein/peptide 40S ribosomal protein S11 /


Mass: 18149.436 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q0E9B6
#12: Protein/peptide 40S ribosomal protein S17 /


Mass: 15313.757 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P17704
#13: Protein/peptide 40S ribosomal protein S15, isoform A / / RE08270p


Mass: 17073.219 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q7JZW2
#14: Protein/peptide 40S ribosomal protein S19a /


Mass: 17327.189 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P39018
#15: Protein/peptide 40S ribosomal protein S3a / / C3 protein


Mass: 30393.160 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P55830
#16: Protein/peptide 40S ribosomal protein SA / / K14 / Laminin receptor homolog / Protein stubarista


Mass: 35384.258 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P38979
#17: Protein/peptide 40S ribosomal protein S21 / / Overgrown hematopoietic organs at 23B


Mass: 9031.153 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O76927
#18: Protein/peptide 40S ribosomal protein S24 /


Mass: 15082.831 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W229
#19: Protein/peptide 40S ribosomal protein S25 /


Mass: 13234.582 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P48588
#20: Protein/peptide 40S ribosomal protein S26 / / DS31


Mass: 13300.712 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P13008
#21: Protein/peptide 40S ribosomal protein S27 /


Mass: 9382.153 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VBU9
#22: Protein/peptide 40S ribosomal protein S28 /


Mass: 7489.732 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W334
#23: Protein/peptide 40S ribosomal protein S3 /


Mass: 27515.143 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q06559
#24: Protein/peptide 40S ribosomal protein S30, isoform A / / Ribosomal protein S30 / isoform B


Mass: 14608.735 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VDH8
#25: Protein/peptide 40S ribosomal protein S27a /


Mass: 9421.213 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P15357
#26: Protein/peptide 40S ribosomal protein S9 /


Mass: 22672.568 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P55935
#27: Protein/peptide 40S ribosomal protein S4 /


Mass: 29191.338 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P41042
#28: Protein/peptide 40S ribosomal protein S2 / / Protein strings of pearls


Mass: 28947.656 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P31009
#29: Protein/peptide 40S ribosomal protein S6 /


Mass: 28478.715 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P29327
#30: Protein/peptide 40S ribosomal protein S5a /


Mass: 25471.375 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q24186
#31: Protein/peptide 40S ribosomal protein S7 /


Mass: 22209.979 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VA91
#32: Protein/peptide 40S ribosomal protein S15Aa /


Mass: 14796.492 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P48149
#33: Protein/peptide 40S ribosomal protein S8 /


Mass: 23814.631 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q8MLY8
#34: Protein/peptide 40S ribosomal protein S16 /


Mass: 16806.703 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W237

-
RNA chain , 6 types, 6 molecules B2BCA5A9A7A8

#36: RNA chain 18S ribosomal RNA /


Mass: 641830.375 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:M21017
#37: RNA chain E-tRNA


Mass: 24249.477 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:K00325
#83: RNA chain 28S ribosomal RNA /


Mass: 1277668.500 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:M21017
#84: RNA chain 2S ribosomal RNA /


Mass: 9665.705 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:M21017
#85: RNA chain 5S ribosomal RNA /


Mass: 38627.906 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:M25016
#86: RNA chain 5.8S ribosomal RNA


Mass: 39616.551 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank:M21017

+
60S ribosomal protein ... , 44 types, 44 molecules CzCKCOCLCVCMCaCNCICDCQCRCACSCTCPCUCXCYCWCZCrChCbCBCFCcCdCeCf...

#38: Protein/peptide 60S ribosomal protein L10a-2 /


Mass: 24404.801 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VTP4
#40: Protein/peptide 60S ribosomal protein L12 /


Mass: 17701.652 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W1B9
#41: Protein/peptide 60S ribosomal protein L13a /


Mass: 23701.166 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VNE9
#42: Protein/peptide 60S ribosomal protein L13 / / BBC1 protein homolog


Mass: 25012.371 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P41126
#43: Protein/peptide 60S ribosomal protein L23 / / L17A


Mass: 14962.603 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P48159
#44: Protein/peptide 60S ribosomal protein L14 /


Mass: 19217.648 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P55841
#45: Protein/peptide 60S ribosomal protein L27a /


Mass: 17070.188 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P41092
#46: Protein/peptide 60S ribosomal protein L15 /


Mass: 24388.592 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O17445
#47: Protein/peptide 60S ribosomal protein L10 / / QM protein homolog / dQM


Mass: 25579.811 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O61231
#48: Protein/peptide 60S ribosomal protein L5 /


Mass: 34101.031 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W5R8
#49: Protein/peptide 60S ribosomal protein L18 /


Mass: 21713.676 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VS34
#50: Protein/peptide 60S ribosomal protein L19 /


Mass: 24065.699 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P36241
#51: Protein/peptide 60S ribosomal protein L8 /


Mass: 27957.730 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9V3G1
#52: Protein/peptide 60S ribosomal protein L18a /


Mass: 21076.750 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P41093
#53: Protein/peptide 60S ribosomal protein L21 / / RH06526p / RE62581p


Mass: 18519.871 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9V9M7
#54: Protein/peptide 60S ribosomal protein L17 /


Mass: 21642.186 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W3W8
#55: Protein/peptide 60S ribosomal protein L22 /


Mass: 30675.709 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P50887
#56: Protein/peptide 60S ribosomal protein L23A / / FI01658p


Mass: 29539.426 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W0A8
#57: Protein/peptide 60S ribosomal protein L26 / / RE17611p


Mass: 17322.293 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VVU2
#58: Protein/peptide 60S ribosomal protein L24 /


Mass: 17568.059 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VJY6
#59: Protein/peptide 60S ribosomal protein L27 /


Mass: 15945.080 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VBN5
#60: Protein/peptide 60S ribosomal protein L28 /


Mass: 16067.016 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VZS5
#61: Protein/peptide 60S ribosomal protein L35 / / FI02809p


Mass: 14491.677 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W499
#62: Protein/peptide 60S ribosomal protein L29 / / L43


Mass: 8945.386 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q24154
#63: Protein/peptide 60S ribosomal protein L3 /


Mass: 47020.062 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O16797
#64: Protein/peptide 60S ribosomal protein L7 /


Mass: 29615.166 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P32100
#65: Protein/peptide 60S ribosomal protein L30 / / RE25263p


Mass: 12253.360 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VJ19
#66: Protein/peptide 60S ribosomal protein L31 /


Mass: 14563.721 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9V597
#67: Protein/peptide 60S ribosomal protein L32 / / Ribosomal protein 49


Mass: 16060.936 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P04359
#68: Protein/peptide 60S ribosomal protein L35A / / RH44960p / RE17737p


Mass: 17701.838 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VNB9
#69: Protein/peptide 60S ribosomal protein L34a / / FI02850p


Mass: 18117.926 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VBH8
#70: Protein/peptide 60S ribosomal protein L36 / / Protein minute(1)1B


Mass: 13541.192 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P49630
#71: Protein/peptide 60S ribosomal protein L37-A /


Mass: 10673.513 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VXX8
#72: Protein/peptide 60S ribosomal protein L38 /


Mass: 8219.802 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9W5N2
#73: Protein/peptide 60S ribosomal protein L39 / / Ribosomal protein 46


Mass: 6318.640 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:O16130
#74: Protein/peptide 60S ribosomal protein L4 / / L1


Mass: 45120.973 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P09180
#75: Protein/peptide 60S ribosomal protein L40 /


Mass: 6200.603 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P18101
#76: Protein/peptide 60S ribosomal protein L41 / / RE63504p


Mass: 3416.400 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q962S2
#77: Protein/peptide 60S ribosomal protein L37a /


Mass: 10335.301 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VMU4
#78: Protein/peptide 60S ribosomal protein L36A / / IP17351p


Mass: 12540.161 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9VLT7
#79: Protein/peptide 60S ribosomal protein L11 /


Mass: 21153.545 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P46222
#80: Protein/peptide 60S ribosomal protein L9 /


Mass: 21425.984 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P50882
#81: Protein/peptide 60S ribosomal protein L6, isoform A /


Mass: 27766.076 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:Q9V9W2
#82: Protein/peptide 60S ribosomal protein L7a /


Mass: 30802.998 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt:P46223

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent ID
280S D. melanogaster ribosomeRIBOSOME1
180S ribosome with E-tRNA, EF-2, and Vig2COMPLEX0
Molecular weightValue: 4 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Mar 10, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 90000 / Calibrated magnification: 90000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: each subvolume
SymmetryPoint symmetry: C1
3D reconstructionMethod: Projection matching / Resolution: 6 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 134500 / Nominal pixel size: 1.2375 / Actual pixel size: 1.2375 / Symmetry type: POINT
Number of atoms included #LASTProtein: 46290 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 46290

+
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.
  • All the functionalities will be ported from the levgacy version.
  • 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