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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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Basic information

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 / homology
Function and homology information


translational elongation / protein kinase activator activity / ribonucleoprotein complex binding / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / cytosolic ribosome / ribosomal small subunit biogenesis / rRNA processing / cytosolic small ribosomal subunit ...translational elongation / protein kinase activator activity / ribonucleoprotein complex binding / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / cytosolic ribosome / ribosomal small subunit biogenesis / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / signal transduction / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S7e / Ribosomal protein L1, conserved site / 60S ribosomal protein L35 / Ribosomal protein L1 ...Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S7e / Ribosomal protein L1, conserved site / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Ribosomal protein S7e / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein L19, eukaryotic / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S28e / Ribosomal protein S7e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L34Ae / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L34e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L19 / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal protein L37ae/L37e / Ribosomal Protein L6, KOW domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal protein L6e / Ribosomal_L19e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L18e / 60S ribosomal protein L6E / Ribosomal L39 protein / Ribosomal protein S28e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L21e signature. / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Ribosomal protein S3, conserved site / Ribosomal protein L5, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein S13, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein L5 / ribosomal L5P family C-terminus
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / 40S ribosomal protein S7 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 / Ribosomal protein L18 / Ribosomal protein L13a / Ribosomal protein L11 / Ribosomal protein / 60S ribosomal protein L6 / 60S ribosomal protein L36 / Ribosomal protein L3 / S28 ribosomal protein / Ribosomal protein L19 / 30S ribosomal protein S3, chloroplastic / Large ribosomal subunit protein uL29 / Putative ribosomal protein S18 / G protein beta subunit
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsBarrio-Garcia, C. / Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. ...Barrio-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.
Citation
Journal: Nature / Year: 2014
Title: Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
Authors: Marko Gogala / Thomas Becker / Birgitta Beatrix / Jean-Paul Armache / Clara Barrio-Garcia / Otto Berninghausen / Roland Beckmann /
Abstract: The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In ...The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of the endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport. The Sec complex consists of three subunits (Sec61α, β and γ) and provides an aqueous environment for the translocation of hydrophilic peptides as well as a lateral opening in the Sec61α subunit that has been proposed to act as a gate for the membrane partitioning of hydrophobic domains. A plug helix and a so-called pore ring are believed to seal the PCC against ion flow and are proposed to rearrange for accommodation of translocating peptides. Several crystal and cryo-electron microscopy structures revealed different conformations of closed and partially open Sec61 and SecY complexes. However, in none of these samples has the translocation state been unambiguously defined biochemically. Here we present cryo-electron microscopy structures of ribosome-bound Sec61 complexes engaged in translocation or membrane insertion of nascent peptides. Our data show that a hydrophilic peptide can translocate through the Sec complex with an essentially closed lateral gate and an only slightly rearranged central channel. Membrane insertion of a hydrophobic domain seems to occur with the Sec complex opening the proposed lateral gate while rearranging the plug to maintain an ion permeability barrier. Taken together, we provide a structural model for the basic activities of the Sec61 complex as a protein-conducting channel.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2010
Title: Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter ...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 /
Abstract: Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, ...Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.
#2: Journal: 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 ...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 /
Abstract: Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than ...Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J5Z, 3J60, 3J61, 3J62
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 15, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 1, 2023Group: Database references / Category: citation_author / database_2
Item: _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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
Polymers3,326,87888
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 method: isolated from a natural source / 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 method: isolated from a natural source / 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 / Source method: isolated from a natural source / Details: messenger RNA / Source: (natural) Triticum aestivum (bread wheat)
#84: RNA chain 60S ribosomal RNA /


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


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


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

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

#4: Protein 40S ribosomal protein S24E / Ribosome


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

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Protein , 3 types, 4 molecules BgCsCtCq

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


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


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


Mass: 34418.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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

#37: Protein 60S ribosomal protein L8E / Ribosome


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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
pH: 7.5
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
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

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 38900 X / 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 / Film or detector model: KODAK SO-163 FILM
Details: Scanned at 5334 dpi on a Heidelberg Primescan Drum Scanner
Image scansNum. digital images: 1374
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: Wiener Filter on 3D volumes (SPIDER)
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection Matching / Resolution: 5.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2108230 / Nominal pixel size: 1.24 Å / Actual pixel size: 1.24 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms0 39411 0 0 39411

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