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- PDB-4v6i: Localization of the small subunit ribosomal proteins into a 6.1 A... -

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Entry
Database: PDB / ID: 4v6i
TitleLocalization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome
Components
  • (40S ribosomal protein ...) x 27
  • (60S acidic ribosomal protein ...) x 3
  • (60S ribosomal protein ...) x 43
  • (Unknown 40S ribosomal protein ...) x 2
  • (Unknown protein) x 2
  • 18S rRNA18S ribosomal RNA
  • 25S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')Messenger RNA
  • P-SITE TRNA ASP
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal proteins / novel ribosomal proteins
Function / homology
Function and homology information


negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / pre-mRNA 5'-splice site binding ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / protein kinase activator activity / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / ribosomal small subunit export from nucleus / ribonucleoprotein complex binding / translation regulator activity / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytoplasmic stress granule / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / response to antibiotic / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site ...Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal L29e protein family / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L1, conserved site / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L1 signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein L1 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L23, N-terminal domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4, KOW domain / Ribosomal_S17 N-terminal / Ribosomal protein L36e signature. / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L14-A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L14-A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein P1A / 60S acidic ribosomal protein P2-alpha / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / 60S ribosomal protein L41-B / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / 40S ribosomal protein S4-B / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L18-A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / 40S ribosomal protein S24-B / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / 40S ribosomal protein S24-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / 60S ribosomal protein L18a / 40S ribosomal protein S30-A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / 60S ribosomal protein L18a
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsArmache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. ...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: 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.
#1: 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
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3IZB, 3IZS, 3IZE, 3IZF
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Other / Category: atom_sites / em_image_scans / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

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Assembly

Deposited unit
Aa: 40S ribosomal protein RACK1 (RACK1)
AA: 40S ribosomal protein rpS0 (S2p)
AB: 40S ribosomal protein rpS3 (S3p)
AD: 40S ribosomal protein rpS4 (S4e)
AC: 40S ribosomal protein rpS9 (S4p)
AE: 40S ribosomal protein rpS2 (S5p)
AG: 40S ribosomal protein rpS7 (S7e)
AF: 40S ribosomal protein rpS5 (S7p)
AH: 40S ribosomal protein rpS22 (S8p)
AI: 40S ribosomal protein rpS16 (S9p)
AJ: 40S ribosomal protein rpS20 (S10p)
AK: 40S ribosomal protein rpS14 (S11p)
AL: 40S ribosomal protein rpS23 (S12p)
AM: 40S ribosomal protein rpS18 (S13p)
AN: 40S ribosomal protein rpS29 (S14p)
AO: 40S ribosomal protein rpS13 (S15p)
AQ: 40S ribosomal protein rpS17 (S17e)
AP: 40S ribosomal protein rpS11 (S17p)
AR: 40S ribosomal protein rpS15 (S19p)
AS: 40S ribosomal protein rpS19 (S19e)
AT: 40S ribosomal protein rpS21 (S21e)
AV: 40S ribosomal protein rpS25 (S25e)
AW: 40S ribosomal protein rpS26 (S26e)
AX: 40S ribosomal protein rpS27 (S27e)
AY: 40S ribosomal protein rpS28 (S28e)
AZ: 40S ribosomal protein rpS30 (S30e)
Ab: Unknown 40S ribosomal protein XS1
Ac: Unknown 40S ribosomal protein XS2
AU: 40S ribosomal protein S24
BA: 60S ribosomal protein rpL1 (L1p)
BB: 60S ribosomal protein rpL2 (L2p)
BC: 60S ribosomal protein rpL3 (L3p)
BD: 60S ribosomal protein rpL4 (L4p)
BE: 60S ribosomal protein rpL11 (L5p)
BG: 60S ribosomal protein rpL6 (L6e)
BF: 60S ribosomal protein rpL9 (L6p)
BH: 60S ribosomal protein rpL8 (L7ae)
Bs: 60S acidic ribosomal protein rpP0 (L10P)
BJ: 60S ribosomal protein rpL12 (L11p)
BK: 60S ribosomal protein rpL16 (L13p)
BN: 60S ribosomal protein rpL14 (L14e)
BM: 60S ribosomal protein rpL23 (L14p)
BP: 60S ribosomal protein rpL15 (L15e)
BO: 60S ribosomal protein rpL28 (L15p)
BR: 60S ribosomal protein rpL18 (L18e)
BT: 60S ribosomal protein rpL19 (L19e)
BU: 60S ribosomal protein rpL21 (L21e)
BW: 60S ribosomal protein rpL22 (L22e)
BV: 60S ribosomal protein rpL17 (L22p)
BX: 60S ribosomal protein rpL25 (L23p)
BZ: 60S ribosomal protein rpL24 (L24e)
BY: 60S ribosomal protein rpL26 (L24p)
Ba: 60S ribosomal protein rpL27 (L27e)
Bd: 60S ribosomal protein rpL29 (L29e)
Bc: 60S ribosomal protein rpL35 (L29p)
Bf: 60S ribosomal protein rpL30 (L30e)
Be: 60S ribosomal protein rpL7 (L30p)
Bg: 60S ribosomal protein rpL31 (L31e)
Bh: 60S ribosomal protein pL32 (L32e)
Bi: 60S ribosomal protein rpL34 (L34e)
Bj: 60S ribosomal protein rpL33 (L35ae)
Bk: 60S ribosomal protein rpL36 (L36e)
Bm: 60S ribosomal protein rpL43 (L37ae)
Bl: 60S ribosomal protein rpL37 (L37e)
Bn: 60S ribosomal protein rpL38 (L38e)
Bo: 60S ribosomal protein rpL39 (L39e)
Bp: 60S ribosomal protein rpL40 (L40e)
Bq: 60S ribosomal protein rpL41 (L41e)
Br: 60S ribosomal protein rpL42 (L44e)
Bx: Unknown protein
By: Unknown protein
Bz: Unknown protein
Bt: 60S acidic ribosomal protein rpP11 (P1)
Bu: 60S acidic ribosomal protein rpP11 (P1)
Bv: 60S acidic ribosomal protein (P2)
Bw: 60S acidic ribosomal protein (P2)
BQ: 60S ribosomal protein rpL5 (L18p)
BL: 60S ribosomal protein rpL13 (L13e)
BS: 60S ribosomal protein rpL20 (L18ae)
BI: 60S ribosomal protein rpL10 (L10e)
CA: 18S rRNA
CB: P-SITE TRNA ASP
CC: MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')
DA: 25S rRNA
DB: 5.8S rRNA
DC: 5S rRNA


Theoretical massNumber of molelcules
Total (without water)3,104,13086
Polymers3,104,13086
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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40S ribosomal protein ... , 27 types, 27 molecules AaAAABADACAEAGAFAHAIAJAKALAMANAOAQAPARASATAVAWAXAYAZAU

#1: Protein 40S ribosomal protein RACK1 (RACK1) / Ribosome


Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011
#2: Protein 40S ribosomal protein rpS0 (S2p) / Ribosome


Mass: 28051.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein rpS3 (S3p) / Ribosome


Mass: 26542.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#4: Protein 40S ribosomal protein rpS4 (S4e) / Ribosome


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05753, UniProt: P0CX35*PLUS
#5: Protein 40S ribosomal protein rpS9 (S4p) / Ribosome


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#6: Protein 40S ribosomal protein rpS2 (S5p) / Ribosome


Mass: 27490.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#7: Protein 40S ribosomal protein rpS7 (S7e) / Ribosome


Mass: 12273.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#8: Protein 40S ribosomal protein rpS5 (S7p) / Ribosome


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#9: Protein 40S ribosomal protein rpS22 (S8p) / Ribosome


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#10: Protein 40S ribosomal protein rpS16 (S9p) / Ribosome


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS
#11: Protein 40S ribosomal protein rpS20 (S10p) / Ribosome


Mass: 13929.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#12: Protein 40S ribosomal protein rpS14 (S11p) / Ribosome


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#13: Protein 40S ribosomal protein rpS23 (S12p) / Ribosome


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32827, UniProt: P0CX30*PLUS
#14: Protein 40S ribosomal protein rpS18 (S13p) / Ribosome


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS
#15: Protein 40S ribosomal protein rpS29 (S14p) / Ribosome


Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057
#16: Protein 40S ribosomal protein rpS13 (S15p) / Ribosome


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#17: Protein 40S ribosomal protein rpS17 (S17e) / Ribosome


Mass: 15820.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407
#18: Protein 40S ribosomal protein rpS11 (S17p) / Ribosome


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS
#19: Protein 40S ribosomal protein rpS15 (S19p) / Ribosome


Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#20: Protein 40S ribosomal protein rpS19 (S19e) / Ribosome


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#21: Protein 40S ribosomal protein rpS21 (S21e) / Ribosome


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0V8
#22: Protein 40S ribosomal protein rpS25 (S25e) / Ribosome


Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#23: Protein 40S ribosomal protein rpS26 (S26e) / Ribosome


Mass: 7932.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein 40S ribosomal protein rpS27 (S27e) / Ribosome


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997
#25: Protein 40S ribosomal protein rpS28 (S28e) / Ribosome


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#26: Protein 40S ribosomal protein rpS30 (S30e) / Ribosome


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12087, UniProt: P0CX33*PLUS
#29: Protein 40S ribosomal protein S24 /


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26782, UniProt: P0CX32*PLUS

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Unknown 40S ribosomal protein ... , 2 types, 2 molecules AbAc

#27: Protein/peptide Unknown 40S ribosomal protein XS1


Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein/peptide Unknown 40S ribosomal protein XS2


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

+
60S ribosomal protein ... , 43 types, 43 molecules BABBBCBDBEBGBFBHBJBKBNBMBPBOBRBTBUBWBVBXBZBYBaBdBcBfBeBgBhBi...

#30: Protein 60S ribosomal protein rpL1 (L1p) / Ribosome


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53030, UniProt: P0CX43*PLUS
#31: Protein 60S ribosomal protein rpL2 (L2p) / Ribosome


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05736, UniProt: P0CX46*PLUS
#32: Protein 60S ribosomal protein rpL3 (L3p) / Ribosome


Mass: 43907.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#33: Protein 60S ribosomal protein rpL4 (L4p) / Ribosome


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#34: Protein 60S ribosomal protein rpL11 (L5p) / Ribosome


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9
#35: Protein 60S ribosomal protein rpL6 (L6e) / Ribosome


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#36: Protein 60S ribosomal protein rpL9 (L6p) / Ribosome


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#37: Protein 60S ribosomal protein rpL8 (L7ae) / Ribosome


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#39: Protein 60S ribosomal protein rpL12 (L11p) / Ribosome


Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17079, UniProt: P0CX53*PLUS
#40: Protein 60S ribosomal protein rpL16 (L13p) / Ribosome


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#41: Protein 60S ribosomal protein rpL14 (L14e) / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: D6VXT1, UniProt: P36105*PLUS
#42: Protein 60S ribosomal protein rpL23 (L14p) / Ribosome


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04451, UniProt: P0CX42*PLUS
#43: Protein 60S ribosomal protein rpL15 (L15e) / Ribosome


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#44: Protein 60S ribosomal protein rpL28 (L15p) / Ribosome


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#45: Protein 60S ribosomal protein rpL18 (L18e) / Ribosome


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07279, UniProt: P0CX50*PLUS
#46: Protein 60S ribosomal protein rpL19 (L19e) / Ribosome


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05735, UniProt: P0CX83*PLUS
#47: Protein 60S ribosomal protein rpL21 (L21e) / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#48: Protein 60S ribosomal protein rpL22 (L22e) / Ribosome


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#49: Protein 60S ribosomal protein rpL17 (L22p) / Ribosome


Mass: 19007.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#50: Protein 60S ribosomal protein rpL25 (L23p) / Ribosome


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#51: Protein 60S ribosomal protein rpL24 (L24e) / Ribosome


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#52: Protein 60S ribosomal protein rpL26 (L24p) / Ribosome


Mass: 13837.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#53: Protein 60S ribosomal protein rpL27 (L27e) / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6
#54: Protein 60S ribosomal protein rpL29 (L29e) / Ribosome


Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747
#55: Protein 60S ribosomal protein rpL35 (L29p) / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#56: Protein 60S ribosomal protein rpL30 (L30e) / Ribosome


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#57: Protein 60S ribosomal protein rpL7 (L30p) / Ribosome


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#58: Protein 60S ribosomal protein rpL31 (L31e) / Ribosome


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#59: Protein 60S ribosomal protein pL32 (L32e) / Ribosome


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#60: Protein 60S ribosomal protein rpL34 (L34e) / Ribosome


Mass: 13343.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#61: Protein 60S ribosomal protein rpL33 (L35ae) / Ribosome


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#62: Protein 60S ribosomal protein rpL36 (L36e) / Ribosome


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#63: Protein 60S ribosomal protein rpL43 (L37ae) / Ribosome


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49631, UniProt: P0CX26*PLUS
#64: Protein 60S ribosomal protein rpL37 (L37e) / Ribosome


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#65: Protein 60S ribosomal protein rpL38 (L38e) / Ribosome


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#66: Protein 60S ribosomal protein rpL39 (L39e) / Ribosome


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#67: Protein 60S ribosomal protein rpL40 (L40e) / Ribosome


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#68: Protein/peptide 60S ribosomal protein rpL41 (L41e) / Ribosome


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05746, UniProt: P0CX86*PLUS
#69: Protein 60S ribosomal protein rpL42 (L44e) / Ribosome


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02405, UniProt: P0CX28*PLUS
#74: Protein 60S ribosomal protein rpL5 (L18p) / Ribosome


Mass: 33792.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#75: Protein 60S ribosomal protein rpL13 (L13e) / Ribosome


Mass: 14485.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#76: Protein 60S ribosomal protein rpL20 (L18ae) / Ribosome


Mass: 20148.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q0JJA0, UniProt: Q943F3*PLUS
#77: Protein 60S ribosomal protein rpL10 (L10e) / Ribosome


Mass: 25410.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805

-
60S acidic ribosomal protein ... , 3 types, 5 molecules BsBtBuBvBw

#38: Protein 60S acidic ribosomal protein rpP0 (L10P)


Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317
#72: Protein 60S acidic ribosomal protein rpP11 (P1)


Mass: 10928.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05318
#73: Protein 60S acidic ribosomal protein (P2)


Mass: 10752.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05319

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Protein/peptide , 2 types, 3 molecules BxByBz

#70: Protein/peptide Unknown protein


Mass: 1805.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#71: Protein/peptide Unknown protein


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
RNA chain , 6 types, 6 molecules CACBCCDADBDC

#78: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#79: RNA chain P-SITE TRNA ASP


Mass: 24135.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: M25599.1
#80: RNA chain MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3') / Messenger RNA


Mass: 3498.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#81: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#82: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#83: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Saccharomyces cerevisiae translating 80S ribosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.8 Å / Num. of particles: 20400 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms28040 0 0 0 28040

+
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