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- PDB-4v6w: Structure of the D. melanogaster 80S ribosome -

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Entry
Database: PDB / ID: 4v6w
TitleStructure of the D. melanogaster 80S ribosome
DescriptorRibosome
KeywordsRIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry
Specimen sourceDrosophila melanogaster / arthropod / Fruit fly / fruit fly / キイロショウジョウバエ /
MethodElectron microscopy (6 Å resolution / Particle / Single particle)
AuthorsAnger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R.
CitationNature, 2013, 497, 80-85

Nature, 2013, 497, 80-85 Yorodumi Papers
Structures of the human and Drosophila 80S ribosome.
Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann

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

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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

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Components

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Polypeptide(L) , 4 types, 4 molecules AzAgAhCq

#1: Polypeptide(L)Elongation factor 2 / EF-2


Mass: 94585.961 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P13060

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)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 / References: UniProt: O18640

Cellular component

Biological process

#35: Polypeptide(L)Vig2, isoform B


Mass: 13542.481 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VBX3

Cellular component

Biological process

#39: Polypeptide(L)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

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40S ribosomal protein ... , 32 types, 32 molecules AUAKAOAXAMASAdANALAR...

#3: Polypeptide(L)40S ribosomal protein S20


Mass: 13513.744 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P55828

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)40S ribosomal protein S10a


Mass: 18259.645 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VB14

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)40S ribosomal protein S14


Mass: 16294.790 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P14130

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)40S ribosomal protein S23


Mass: 16054.750 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q8T3U2

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)40S ribosomal protein S12


Mass: 15191.617 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P80455

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)40S ribosomal protein S18


Mass: 17649.631 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P41094

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)40S ribosomal protein S29


Mass: 6603.676 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VH69

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)40S ribosomal protein S13


Mass: 17216.436 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q03334

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)40S ribosomal protein S11


Mass: 18149.436 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q0E9B6

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)40S ribosomal protein S17


Mass: 15313.757 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P17704

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)40S ribosomal protein S15, isoform A / RE08270p


Mass: 17073.219 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q7JZW2

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)40S ribosomal protein S19a


Mass: 17327.189 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P39018

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)40S ribosomal protein S3a / C3 protein


Mass: 30393.160 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P55830

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)40S ribosomal protein SA / K14 / Laminin receptor homolog / Protein stubarista


Mass: 35384.258 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P38979

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • multicellular organism development (GO: 0007275)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
#17: Polypeptide(L)40S ribosomal protein S21 / Overgrown hematopoietic organs at 23B


Mass: 9031.153 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: O76927

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • lymph gland development (GO: 0048542)
  • regulation of cell proliferation (GO: 0042127)
  • regulation of translation (GO: 0006417)
#18: Polypeptide(L)40S ribosomal protein S24


Mass: 15082.831 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W229

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#19: Polypeptide(L)40S ribosomal protein S25


Mass: 13234.582 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P48588

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)40S ribosomal protein S26 / DS31


Mass: 13300.712 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P13008

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)40S ribosomal protein S27


Mass: 9382.153 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VBU9

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)40S ribosomal protein S28


Mass: 7489.732 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W334

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)40S ribosomal protein S3


Mass: 27515.143 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q06559

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)40S ribosomal protein S30, isoform A / Ribosomal protein S30 / isoform B


Mass: 14608.735 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VDH8

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)40S ribosomal protein S27a


Mass: 9421.213 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P15357

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)40S ribosomal protein S9


Mass: 22672.568 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P55935

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)40S ribosomal protein S4


Mass: 29191.338 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P41042

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)40S ribosomal protein S2 / Protein strings of pearls


Mass: 28947.656 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P31009

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)40S ribosomal protein S6


Mass: 28478.715 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P29327

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)40S ribosomal protein S5a


Mass: 25471.375 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q24186

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)40S ribosomal protein S7


Mass: 22209.979 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VA91

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)40S ribosomal protein S15Aa


Mass: 14796.492 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P48149

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)40S ribosomal protein S8


Mass: 23814.631 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q8MLY8

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)40S ribosomal protein S16


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

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)

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RNA chain , 6 types, 6 molecules B2BCA5A9A7A8

#36: RNA chain18S ribosomal RNA


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


Mass: 24249.477 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: GenBank: K00325
#83: RNA chain28S ribosomal RNA


Mass: 1277668.500 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: GenBank: M21017
#84: RNA chain2S ribosomal RNA


Mass: 9665.705 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: GenBank: M21017
#85: RNA chain5S ribosomal RNA


Mass: 38627.906 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: GenBank: M25016
#86: RNA chain5.8S ribosomal RNA


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

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60S ribosomal protein ... , 44 types, 44 molecules CzCKCOCLCVCMCaCNCICD...

#38: Polypeptide(L)60S ribosomal protein L10a-2


Mass: 24404.801 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VTP4

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein L12


Mass: 17701.652 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W1B9

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein L13a


Mass: 23701.166 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VNE9

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)60S ribosomal protein L13 / BBC1 protein homolog


Mass: 25012.371 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P41126

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein L23 / L17A


Mass: 14962.603 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P48159

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein L14


Mass: 19217.648 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P55841

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L27a


Mass: 17070.188 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P41092

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)60S ribosomal protein L15


Mass: 24388.592 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: O17445

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)60S ribosomal protein L10 / QM protein homolog / dQM


Mass: 25579.811 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: O61231

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)60S ribosomal protein L5


Mass: 34101.031 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W5R8

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)60S ribosomal protein L18


Mass: 21713.676 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VS34

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)60S ribosomal protein L19


Mass: 24065.699 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P36241

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)60S ribosomal protein L8


Mass: 27957.730 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9V3G1

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)60S ribosomal protein L18a


Mass: 21076.750 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P41093

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)60S ribosomal protein L21 / RH06526p / RE62581p


Mass: 18519.871 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9V9M7

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)60S ribosomal protein L17


Mass: 21642.186 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W3W8

Cellular component

Molecular function

Biological process

#55: Polypeptide(L)60S ribosomal protein L22


Mass: 30675.709 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P50887

Cellular component

Molecular function

Biological process

#56: Polypeptide(L)60S ribosomal protein L23A / FI01658p


Mass: 29539.426 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W0A8

Cellular component

Molecular function

Biological process

#57: Polypeptide(L)60S ribosomal protein L26 / RE17611p


Mass: 17322.293 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VVU2

Cellular component

Molecular function

Biological process

#58: Polypeptide(L)60S ribosomal protein L24


Mass: 17568.059 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VJY6

Cellular component

Molecular function

Biological process

#59: Polypeptide(L)60S ribosomal protein L27


Mass: 15945.080 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VBN5

Cellular component

Molecular function

Biological process

#60: Polypeptide(L)60S ribosomal protein L28


Mass: 16067.016 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VZS5

Cellular component

Molecular function

Biological process

#61: Polypeptide(L)60S ribosomal protein L35 / FI02809p


Mass: 14491.677 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W499

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
#62: Polypeptide(L)60S ribosomal protein L29 / L43


Mass: 8945.386 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q24154

Cellular component

Molecular function

Biological process

#63: Polypeptide(L)60S ribosomal protein L3


Mass: 47020.062 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: O16797

Cellular component

Molecular function

Biological process

#64: Polypeptide(L)60S ribosomal protein L7


Mass: 29615.166 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P32100

Cellular component

Molecular function

Biological process

#65: Polypeptide(L)60S ribosomal protein L30 / RE25263p


Mass: 12253.360 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VJ19

Cellular component

Molecular function

Biological process

#66: Polypeptide(L)60S ribosomal protein L31


Mass: 14563.721 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9V597

Cellular component

Molecular function

Biological process

#67: Polypeptide(L)60S ribosomal protein L32 / Ribosomal protein 49


Mass: 16060.936 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P04359

Cellular component

Molecular function

Biological process

#68: Polypeptide(L)60S ribosomal protein L35A / RH44960p / RE17737p


Mass: 17701.838 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VNB9

Cellular component

Molecular function

Biological process

#69: Polypeptide(L)60S ribosomal protein L34a / FI02850p


Mass: 18117.926 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VBH8

Cellular component

Molecular function

Biological process

#70: Polypeptide(L)60S ribosomal protein L36 / Protein minute(1)1B


Mass: 13541.192 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P49630

Cellular component

Molecular function

Biological process

#71: Polypeptide(L)60S ribosomal protein L37-A


Mass: 10673.513 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VXX8

Cellular component

Molecular function

Biological process

#72: Polypeptide(L)60S ribosomal protein L38


Mass: 8219.802 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9W5N2

Cellular component

Molecular function

Biological process

#73: Polypeptide(L)60S ribosomal protein L39 / Ribosomal protein 46


Mass: 6318.640 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: O16130

Cellular component

Molecular function

Biological process

#74: Polypeptide(L)60S ribosomal protein L4 / L1


Mass: 45120.973 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P09180

Cellular component

Molecular function

Biological process

#75: Polypeptide(L)60S ribosomal protein L40


Mass: 6200.603 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P18101

Cellular component

Molecular function

Biological process

#76: Polypeptide(L)60S ribosomal protein L41 / RE63504p


Mass: 3416.400 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q962S2

Cellular component

Molecular function

Biological process

#77: Polypeptide(L)60S ribosomal protein L37a


Mass: 10335.301 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VMU4

Cellular component

Molecular function

Biological process

#78: Polypeptide(L)60S ribosomal protein L36A / IP17351p


Mass: 12540.161 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9VLT7

Cellular component

Molecular function

Biological process

#79: Polypeptide(L)60S ribosomal protein L11


Mass: 21153.545 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P46222

Cellular component

Molecular function

Biological process

#80: Polypeptide(L)60S ribosomal protein L9


Mass: 21425.984 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: P50882

Cellular component

Molecular function

Biological process

#81: Polypeptide(L)60S ribosomal protein L6, isoform A


Mass: 27766.076 Da / Num. of mol.: 1 / Source: (natural) Drosophila melanogaster / References: UniProt: Q9V9W2

Cellular component

Molecular function

Biological process

#82: Polypeptide(L)60S ribosomal protein L7a


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

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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).

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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 FIELD / 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

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Processing

EM softwareName: SPIDER / Category: 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

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About Yorodumi

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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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

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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

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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