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- PDB-4v7e: Model of the small subunit RNA based on a 5.5 A cryo-EM map of Tr... -

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Entry
Database: PDB / ID: 4v7e
TitleModel of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 45
  • 18S ribosomal RNA
  • 5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • 60S ribosomal RNA
  • Acidic ribosomal protein P2
  • P-site tRNA
  • RACK1Receptor for activated C kinase 1
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal RNA / rRNA / RNA expansion segments
Function / homology60s Acidic ribosomal protein / Ribosomal protein S3, C-terminal domain / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein P1/P2, N-terminal domain / Ribosomal protein L14p/L23e ...60s Acidic ribosomal protein / Ribosomal protein S3, C-terminal domain / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein P1/P2, N-terminal domain / Ribosomal protein L14p/L23e / WD40-repeat-containing domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / WD domain, G-beta repeat / Ribosomal protein S13/S18 / Ribosomal protein L13 / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L1p/L10e family / 30s ribosomal protein S13, C-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L13, conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L12 family / Ribosomal protein L29/L35 superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / ribosomal L5P family C-terminus / Ribosomal L29 protein / Ribosomal protein L18e, conserved site / Ribosomal protein L34e signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L13 signature. / Ribosomal protein S7e signature. / Ribosomal protein S28e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L18e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30 signature. / Ribosomal protein L21e signature. / Ribosomal protein L36e signature. / Ribosomal protein L1 signature. / Trp-Asp (WD) repeats profile. / Ribosomal protein S13 family profile. / Trp-Asp (WD) repeats circular profile. / Type-2 KH domain profile. / Ribosomal protein S13 signature. / Ribosomal protein S3 signature. / Ribosomal L39 protein / Ribosomal protein L19e / Ribosomal protein L21e / Ribosomal protein L36e / Ribosomal protein L6e / Ribosomal protein L34e / Ribosomal protein S28e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S7e / Ribosomal L37ae protein family / Ribosomal protein L19e signature. / KH domain / Ribosomal L30 N-terminal domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L14 signature. / Ribosomal protein L39e signature. / Ribosomal protein L5 signature. / Ribosomal protein L3 signature. / Ribosomal protein L5 domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L18e/L15P / G-protein, beta subunit / Ribosomal protein L13 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / K Homology domain, type 2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L37ae / Ribosomal protein L1 / Ribosomal protein L5 / Ribosomal protein S13 / Ribosomal protein L29/L35 / WD40 repeat / Ribosomal protein S3, C-terminal / Ribosomal protein L34Ae / Ribosomal protein S14 / Ribosomal protein L21e / 60S ribosomal protein L6E / Ribosomal protein L3 / Ribosomal protein S7e
Function and homology information
Specimen sourceTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.5 Å resolution
AuthorsBarrio-Garcia, C. / Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. / Marquez, V. / Mielke, T. / Thomm, M. / Berninghausen, O. / Beatrix, B. / Soeding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2010
Title: Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter Marquez / Thorsten Mielke / Michael Thomm / Otto Berninghausen / Birgitta Beatrix / Johannes Söding / Eric Westhof / Daniel N Wilson / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 22, 2013 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 15, 2015Structure modelOther

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1780
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
Ad: 18S ribosomal RNA
Ae: P-site tRNA
Af: 5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'
BY: 40S ribosomal protein S24E
BI: 40S ribosomal protein S8E
BK: 40S ribosomal protein S10E
BM: 40S ribosomal protein S12E
Bf: 40S ribosomal protein S31e
BX: 40S ribosomal protein S12
Bg: RACK1
BD: 40S ribosomal protein S3
BE: 40S ribosomal protein S4E
BF: 40S ribosomal protein S7
BQ: 40S ribosomal protein S9
BU: 40S ribosomal protein S10
BO: 40S ribosomal protein S11
BS: 40S ribosomal protein S13
BN: 40S ribosomal protein S15
BL: 40S ribosomal protein S17
BT: 40S ribosomal protein S19E
BP: 40S ribosomal protein S19
BZ: 40S ribosomal protein S25E
Bc: 40S ribosomal protein S28E
BW: 40S ribosomal protein S8
Bd: 40S ribosomal protein S14
Bb: 40S ribosomal protein S27E
Be: 40S ribosomal protein S30E
BA: 40S ribosomal protein S2
BR: 40S ribosomal protein S17E
BB: 40S ribosomal protein S1E
BV: 40S ribosomal protein S21E
Ba: 40S ribosomal protein S26E
BJ: 40S ribosomal protein S4
BC: 40S ribosomal protein S5
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7E
CG: 60S ribosomal protein L8E
CT: 60S ribosomal protein L21E
CZ: 60S ribosomal protein L27E
Cz: 60S ribosomal protein L1
CA: 60S ribosomal protein L2
CJ: 60S ribosomal protein L5
CH: 60S ribosomal protein L6
CV: 60S ribosomal protein L14
CN: 60S ribosomal protein L15E
Ca: 60S ribosomal protein L15
CQ: 60S ribosomal protein L18E
CD: 60S ribosomal protein L18
CR: 60S ribosomal protein L19E
CP: 60S ribosomal protein L22
CX: 60S ribosomal protein L23
CW: 60S ribosomal protein L24E
CY: 60S ribosomal protein L24
Cr: 60S ribosomal protein L28E
Cc: 60S ribosomal protein L30E
Cd: 60S ribosomal protein L31E
Ce: 60S ribosomal protein L32E
Cj: 60S ribosomal protein L37E
Cl: 60S ribosomal protein L39E
Co: 60S ribosomal protein L44E
CM: 60S ribosomal protein L14E
CS: 60S ribosomal protein L20
CU: 60S ribosomal protein L22E
Ci: 60S ribosomal protein L36E
CK: 60S ribosomal protein L11
Cu: 60S ribosomal protein P1
Cv: 60S ribosomal protein P1
Cs: Acidic ribosomal protein P2
Ct: Acidic ribosomal protein P2
Ch: 60S ribosomal protein L29
CF: 60S ribosomal protein L30
Cq: 60S acidic ribosomal protein P0
CB: 60S ribosomal protein L3
CC: 60S ribosomal protein L4
CO: 60S ribosomal protein L13
Cp: 60S ribosomal protein L43E
CI: 60S ribosomal protein L16
Cn: 60S ribosomal protein L41E
Cm: 60S ribosomal protein L40E
CL: 60S ribosomal protein L13E
CE: 60S ribosomal protein L6E
Cf: 60S ribosomal protein L33E
Ck: 60S ribosomal protein L38E
Cb: 60S ribosomal protein L29E
Cg: 60S ribosomal protein L34E
Aa: 60S ribosomal RNA
Ac: 5.8S ribosomal RNA
Ab: 5S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)3,326,87888
Polyers3,326,87888
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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RNA chain , 6 types, 6 molecules AdAeAfAaAcAb

#1: RNA chain 18S ribosomal RNA /


Mass: 583613.562 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: AY049040.1
#2: RNA chain P-site tRNA


Mass: 24135.262 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: M25599.1
#3: RNA chain 5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'


Mass: 3498.178 Da / Num. of mol.: 1 / Details: messenger RNA / Source: (natural) Triticum aestivum (bread wheat)
#84: RNA chain 60S ribosomal RNA /


Mass: 1097289.250 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#85: RNA chain 5.8S ribosomal RNA /


Mass: 51535.613 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#86: RNA chain 5S ribosomal RNA /


Mass: 38716.957 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: X06094.1

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

#4: Protein/peptide 40S ribosomal protein S24E / Ribosome


Mass: 15788.734 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#5: Protein/peptide 40S ribosomal protein S8E / Ribosome


Mass: 24883.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#6: Protein/peptide 40S ribosomal protein S10E / Ribosome


Mass: 20292.812 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#7: Protein/peptide 40S ribosomal protein S12E / Ribosome


Mass: 18404.377 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#8: Protein/peptide 40S ribosomal protein S31e / Ribosome


Mass: 17720.691 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#9: Protein/peptide 40S ribosomal protein S12 /


Mass: 15696.476 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#11: Protein/peptide 40S ribosomal protein S3 /


Mass: 23255.113 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L804
#12: Protein/peptide 40S ribosomal protein S4E / Ribosome


Mass: 29922.018 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#13: Protein/peptide 40S ribosomal protein S7 /


Mass: 21249.539 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#14: Protein/peptide 40S ribosomal protein S9 /


Mass: 16852.977 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#15: Protein/peptide 40S ribosomal protein S10 /


Mass: 14070.350 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#16: Protein/peptide 40S ribosomal protein S11 /


Mass: 16351.802 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#17: Protein/peptide 40S ribosomal protein S13 /


Mass: 17702.686 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L806
#18: Protein/peptide 40S ribosomal protein S15 /


Mass: 17152.379 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#19: Protein/peptide 40S ribosomal protein S17 /


Mass: 18027.361 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#20: Protein/peptide 40S ribosomal protein S19E / Ribosome


Mass: 16414.846 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#21: Protein/peptide 40S ribosomal protein S19 /


Mass: 17449.520 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#22: Protein/peptide 40S ribosomal protein S25E / Ribosome


Mass: 11944.909 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#23: Protein/peptide 40S ribosomal protein S28E / Ribosome


Mass: 7477.787 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X9K4
#24: Protein/peptide 40S ribosomal protein S8 /


Mass: 14825.377 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#25: Protein/peptide 40S ribosomal protein S14 /


Mass: 6392.440 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K3
#26: Protein/peptide 40S ribosomal protein S27E / Ribosome


Mass: 9542.145 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#27: Protein/peptide 40S ribosomal protein S30E / Ribosome


Mass: 6953.253 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#28: Protein/peptide 40S ribosomal protein S2 /


Mass: 28723.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#29: Protein/peptide 40S ribosomal protein S17E / Ribosome


Mass: 16461.135 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#30: Protein/peptide 40S ribosomal protein S1E / Ribosome


Mass: 29781.682 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#31: Protein/peptide 40S ribosomal protein S21E / Ribosome


Mass: 9266.369 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#32: Protein/peptide 40S ribosomal protein S26E / Ribosome


Mass: 15029.448 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#33: Protein/peptide 40S ribosomal protein S4 /


Mass: 22629.166 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#34: Protein/peptide 40S ribosomal protein S5 /


Mass: 28859.619 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#35: Protein/peptide 40S ribosomal protein S6 /


Mass: 28106.990 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#36: Protein/peptide 40S ribosomal protein S7E / Ribosome


Mass: 21902.414 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K2

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Protein/peptide , 3 types, 4 molecules BgCsCtCq

#10: Protein/peptide RACK1 / Receptor for activated C kinase 1


Mass: 41794.809 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8LNY6
#67: Protein/peptide Acidic ribosomal protein P2


Mass: 11596.995 Da / Num. of mol.: 2 / Source: (natural) Triticum aestivum (bread wheat)
#70: Protein/peptide 60S acidic ribosomal protein P0


Mass: 34418.574 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)

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60S ribosomal protein ... , 45 types, 46 molecules CGCTCZCzCACJCHCVCNCaCQCDCRCPCXCWCYCrCcCdCeCjClCoCMCSCUCiCKCu...

#37: Protein/peptide 60S ribosomal protein L8E / Ribosome


Mass: 29236.938 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#38: Protein/peptide 60S ribosomal protein L21E / Ribosome


Mass: 18719.801 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: F4YWL9
#39: Protein/peptide 60S ribosomal protein L27E / Ribosome


Mass: 15508.620 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#40: Protein/peptide 60S ribosomal protein L1 /


Mass: 24604.240 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L3
#41: Protein/peptide 60S ribosomal protein L2 /


Mass: 28309.662 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#42: Protein/peptide 60S ribosomal protein L5 /


Mass: 20727.090 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L2
#43: Protein/peptide 60S ribosomal protein L6 /


Mass: 21382.818 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#44: Protein/peptide 60S ribosomal protein L14 /


Mass: 15040.856 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K4
#45: Protein/peptide 60S ribosomal protein L15E / Ribosome


Mass: 23760.797 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#46: Protein/peptide 60S ribosomal protein L15 /


Mass: 15834.768 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#47: Protein/peptide 60S ribosomal protein L18E / Ribosome


Mass: 21379.338 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L0
#48: Protein/peptide 60S ribosomal protein L18 /


Mass: 34723.168 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#49: Protein/peptide 60S ribosomal protein L19E / Ribosome


Mass: 24485.947 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7XY20
#50: Protein/peptide 60S ribosomal protein L22 /


Mass: 19536.494 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#51: Protein/peptide 60S ribosomal protein L23 /


Mass: 17091.447 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#52: Protein/peptide 60S ribosomal protein L24E / Ribosome


Mass: 18504.867 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#53: Protein/peptide 60S ribosomal protein L24 /


Mass: 16971.777 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#54: Protein/peptide 60S ribosomal protein L28E / Ribosome


Mass: 16639.441 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#55: Protein/peptide 60S ribosomal protein L30E / Ribosome


Mass: 12294.396 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K9
#56: Protein/peptide 60S ribosomal protein L31E / Ribosome


Mass: 14092.330 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#57: Protein/peptide 60S ribosomal protein L32E / Ribosome


Mass: 15740.655 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#58: Protein/peptide 60S ribosomal protein L37E / Ribosome


Mass: 10823.657 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#59: Protein/peptide 60S ribosomal protein L39E / Ribosome


Mass: 6528.786 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K7
#60: Protein/peptide 60S ribosomal protein L44E / Ribosome


Mass: 12174.439 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#61: Protein/peptide 60S ribosomal protein L14E / Ribosome


Mass: 15418.365 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#62: Protein/peptide 60S ribosomal protein L20 /


Mass: 21444.225 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#63: Protein/peptide 60S ribosomal protein L22E / Ribosome


Mass: 14443.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#64: Protein/peptide 60S ribosomal protein L36E / Ribosome


Mass: 12563.044 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L5
#65: Protein/peptide 60S ribosomal protein L11 /


Mass: 17775.705 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#66: Protein/peptide 60S ribosomal protein P1 /


Mass: 11204.584 Da / Num. of mol.: 2 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K5
#68: Protein/peptide 60S ribosomal protein L29 /


Mass: 14401.041 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L805
#69: Protein/peptide 60S ribosomal protein L30 /


Mass: 28175.119 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K6
#71: Protein/peptide 60S ribosomal protein L3 /


Mass: 44720.387 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X744
#72: Protein/peptide 60S ribosomal protein L4 /


Mass: 44822.043 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#73: Protein/peptide 60S ribosomal protein L13 /


Mass: 23581.172 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L1
#74: Protein/peptide 60S ribosomal protein L43E / Ribosome


Mass: 10266.146 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: D8L9P6
#75: Protein/peptide 60S ribosomal protein L16 /


Mass: 25400.791 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#76: Protein/peptide 60S ribosomal protein L41E / Ribosome


Mass: 3445.437 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#77: Protein/peptide 60S ribosomal protein L40E / Ribosome


Mass: 6295.639 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#78: Protein/peptide 60S ribosomal protein L13E / Ribosome


Mass: 24070.221 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#79: Protein/peptide 60S ribosomal protein L6E / Ribosome


Mass: 24589.756 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L4
#80: Protein/peptide 60S ribosomal protein L33E / Ribosome


Mass: 12684.730 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#81: Protein/peptide 60S ribosomal protein L38E / Ribosome


Mass: 8053.604 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#82: Protein/peptide 60S ribosomal protein L29E / Ribosome


Mass: 7069.020 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat)
#83: Protein/peptide 60S ribosomal protein L34E / Ribosome


Mass: 13808.402 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K8

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeParent ID
1Programmed Wheat Germ 80S RibosomeRIBOSOME0
2Tritcum aestivum 80S ribosomeRIBOSOME1
Molecular weightValue: 4.2 MDa / Experimental value: YES
Buffer solutionName: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/mL cycloheximide, 1 mM DTT, 0.01% Nikkol
Details: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/mL cycloheximide, 1 mM DTT, 0.01% Nikkol
pH: 7.5
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil Grid with 2 nm carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 10 seconds (using 2 layers of filter paper) before plunging into liquid ethane (FEI VITROBOT).
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 38900 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: FEI Polara Cartridge System
Image recordingElectron dose: 25 e/Å2
Details: Scanned at 5334 dpi on a Heidelberg Primescan Drum Scanner
Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 1374
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: 3D reconstruction
CTF correctionDetails: Wiener Filter on 3D volumes (SPIDER)
SymmetryPoint symmetry: C1
3D reconstructionMethod: Projection Matching / Resolution: 5.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 2108230 / Nominal pixel size: 1.24 / Actual pixel size: 1.24 / Symmetry type: POINT
Number of atoms included #LASTProtein: 0 / Nucleic acid: 39411 / Ligand: 0 / Solvent: 0 / Total: 39411

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