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- PDB-4adx: The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Co... -

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Basic information

Entry
Database: PDB / ID: 4adx
TitleThe Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6
Components
  • 23S Ribosomal RNA EXPANSION SEGMENTS
  • 23S ribosomal RNA
  • 5S Ribosomal RNA
  • AIF6
  • RPL10E
  • RPL13
  • RPL14
  • RPL14E
  • RPL15
  • RPL15E
  • RPL1860S ribosomal protein L18
  • RPL18E
  • RPL19E
  • RPL2
  • RPL21E
  • RPL2260S ribosomal protein L22
  • RPL23
  • RPL24
  • RPL24E
  • RPL29
  • RPL3
  • RPL30
  • RPL30E
  • RPL31E
  • RPL32E
  • RPL34E
  • RPL37AE
  • RPL37E
  • RPL39E
  • RPL40E
  • RPL44E
  • RPL460S ribosomal protein L4
  • RPL5
  • RPL6
  • RPL7AE
  • RPLX
KeywordsRIBOSOME / PROTEIN SYNTHESIS
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleotide binding / DNA repair / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea ...Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Helix-hairpin-helix domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L44e / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L30/YlxQ / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal L40e family / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L10e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L19e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e signature. / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L14e domain / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L32e, conserved site / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L14 / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L14 / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L14, KOW motif / Ribosomal protein L24e-related / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L19e / Ribosomal protein L18e / Ribosomal L39 protein / Ribosomal protein L37e / Ribosomal protein L24e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL20 / Translation initiation factor 6 / Large ribosomal subunit protein eL34 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL22 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL20 / Translation initiation factor 6 / Large ribosomal subunit protein eL34 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
Model type detailsCA ATOMS ONLY, CHAIN Z, H, J, K, L, M, N, O, P, S, V, T, R, X, E, B, C, A, D, F, 3, Q, U, I, W, Y, ...CA ATOMS ONLY, CHAIN Z, H, J, K, L, M, N, O, P, S, V, T, R, X, E, B, C, A, D, F, 3, Q, U, I, W, Y, 1, 2, 4, 5, 6, 7, G ; P ATOMS ONLY, CHAIN 9, 0, 8
AuthorsGreber, B.J. / Boehringer, D. / Godinic-Mikulcic, V. / Crnkovic, A. / Ibba, M. / Weygand-Durasevic, I. / Ban, N.
CitationJournal: J Mol Biol / Year: 2012
Title: Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution.
Authors: Basil J Greber / Daniel Boehringer / Vlatka Godinic-Mikulcic / Ana Crnkovic / Michael Ibba / Ivana Weygand-Durasevic / Nenad Ban /
Abstract: Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains ...Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea.
History
DepositionJan 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Mar 20, 2013Group: Other / Source and taxonomy
Revision 1.3Aug 23, 2017Group: Data collection / Structure summary / Category: em_imaging / em_software / entity
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id / _entity.pdbx_description / _entity.src_method

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2012
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 23S ribosomal RNA
1: RPL37E
2: RPL39E
3: RPL44E
4: RPL34E
5: RPL40E
6: RPL30E
7: RPL14E
8: 23S Ribosomal RNA EXPANSION SEGMENTS
9: 5S Ribosomal RNA
A: RPL2
B: RPL3
C: RPL4
D: RPL5
E: RPL6
F: RPL7AE
G: RPLX
H: RPL10E
I: AIF6
J: RPL13
K: RPL14
L: RPL15
M: RPL15E
N: RPL18
O: RPL18E
P: RPL19E
Q: RPL21E
R: RPL22
S: RPL23
T: RPL24
U: RPL24E
V: RPL29
W: RPL30
X: RPL31E
Y: RPL32E
Z: RPL37AE


Theoretical massNumber of molelcules
Total (without water)1,551,05136
Polymers1,551,05136
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 , 3 types, 3 molecules 089

#1: RNA chain 23S ribosomal RNA / / Coordinate model: P atoms only


Mass: 946407.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H
#9: RNA chain 23S Ribosomal RNA EXPANSION SEGMENTS / Coordinate model: P atoms only


Mass: 43052.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H
#10: RNA chain 5S Ribosomal RNA / / Coordinate model: P atoms only


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H

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Protein , 32 types, 32 molecules 134567ABCDEFGHIJKLMNOPQRSTUVWXYZ

#2: Protein RPL37E / Coordinate model: Cα atoms only


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P32410*PLUS
#4: Protein RPL44E / Coordinate model: Cα atoms only


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / References: UniProt: P32411*PLUS
#5: Protein RPL34E / Coordinate model: Cα atoms only


Mass: 14071.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P0DJ23*PLUS
#6: Protein RPL40E / Coordinate model: Cα atoms only


Mass: 14599.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P0DJ25*PLUS
#7: Protein RPL30E / Coordinate model: Cα atoms only


Mass: 11368.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P0DJ59*PLUS
#8: Protein RPL14E / Coordinate model: Cα atoms only


Mass: 14629.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: Q24C27*PLUS
#11: Protein RPL2 / Coordinate model: Cα atoms only


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P20276*PLUS
#12: Protein RPL3 / Coordinate model: Cα atoms only


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P20279*PLUS
#13: Protein RPL4 / 60S ribosomal protein L4 / Coordinate model: Cα atoms only


Mass: 26457.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12735*PLUS
#14: Protein RPL5 / Coordinate model: Cα atoms only


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14124*PLUS
#15: Protein RPL6 / Coordinate model: Cα atoms only


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14135*PLUS
#16: Protein RPL7AE / Coordinate model: Cα atoms only


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12743*PLUS
#17: Protein RPLX / Coordinate model: Cα atoms only


Mass: 9297.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: O27647*PLUS
#18: Protein RPL10E / Coordinate model: Cα atoms only


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P60617*PLUS
#19: Protein AIF6 / Coordinate model: Cα atoms only


Mass: 22669.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: O27648*PLUS
#20: Protein RPL13 / Coordinate model: Cα atoms only


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H
#21: Protein RPL14 / Coordinate model: Cα atoms only


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P22450*PLUS
#22: Protein RPL15 / Coordinate model: Cα atoms only


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12737*PLUS
#23: Protein RPL15E / Coordinate model: Cα atoms only


Mass: 22404.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P60618*PLUS
#24: Protein RPL18 / 60S ribosomal protein L18 / Coordinate model: Cα atoms only


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14123*PLUS
#25: Protein RPL18E / Coordinate model: Cα atoms only


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12733*PLUS
#26: Protein RPL19E / Coordinate model: Cα atoms only


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14119*PLUS
#27: Protein RPL21E / Coordinate model: Cα atoms only


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12734*PLUS
#28: Protein RPL22 / 60S ribosomal protein L22 / Coordinate model: Cα atoms only


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P10970*PLUS
#29: Protein RPL23 / Coordinate model: Cα atoms only


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12732*PLUS
#30: Protein RPL24 / Coordinate model: Cα atoms only


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P10972*PLUS
#31: Protein RPL24E / Coordinate model: Cα atoms only


Mass: 7364.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14116*PLUS
#32: Protein RPL29 / Coordinate model: Cα atoms only


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P10971*PLUS
#33: Protein RPL30 / Coordinate model: Cα atoms only


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P14121*PLUS
#34: Protein RPL31E / Coordinate model: Cα atoms only


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P18138*PLUS
#35: Protein RPL32E / Coordinate model: Cα atoms only


Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P12736*PLUS
#36: Protein RPL37AE / Coordinate model: Cα atoms only


Mass: 10189.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P60619*PLUS

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Protein/peptide , 1 types, 1 molecules 2

#3: Protein/peptide RPL39E / Coordinate model: Cα atoms only


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: DELTA H / References: UniProt: P22452*PLUS

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Details

Sequence detailsTHE SOURCE ORGANISM FOR THE RIBOSOMES UNDER STUDY EMD-2012 IS METHANOTHERMOBACTER ...THE SOURCE ORGANISM FOR THE RIBOSOMES UNDER STUDY EMD-2012 IS METHANOTHERMOBACTER THERMAUTOTROPHICUS.THE FITTED MODEL FOR CHAIN 0 COMES FROM THE HALOARCULA MARISMORTUI X-RAY CRYSTAL STRUCTURE.THE CRYO-EM MAPS OF THE METHANOTHERMOBACTER 50S SUBUNIT WERE INTERPRETED BY RIGID BODY DOCKING OF THE HIGH RESOLUTION STRUCTURE OF THE HALOARCULA MARISMORTUI 50S SUBUNIT. THE CHAIN 8 MODEL SEQUENCE CORRESPONDS TO RRNA EXPANSION SEGMENTS OF THE METHANOTHERMOBACTER 23S RRNA.HENCE, EVEN THOUGH CHAIN 8 IS COMPOSED OF SEVERAL FRAGMENTS, ALL THESE FRAGMENTS BELONG TO THE SAME METHANOTHERMOBACTER RRNA MOLECULE. 3 DIFFERENT TEMPLATES WERE USED AS THE SOURCE FOR THE MODEL. THE SOURCES ARE AS FOLLOWS - PDB ID 4A17 (CHAIN 2, NUCLEOTIDES 115-134), 4A19(CHAIN 1, NUCLEOTIDES 125-144, 1645-1678, 1827-1849, 3302-3317), 3O58 (CHAIN 1, NUCLEOTIDES 1753-1772).

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 50S RIBOSOMAL SUBUNIT IN COMPLEX WITH ARCHAEAL IF6 / Type: RIBOSOME
Buffer solutionName: 20 MM TRIS-HCL PH 8.0, 50 MM NH4CL, 20 MM MGCL2 / pH: 8 / Details: 20 MM TRIS-HCL PH 8.0, 50 MM NH4CL, 20 MM MGCL2
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: MANUAL PLUNGING INTO LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 62000 X / Calibrated magnification: 83000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 553
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2IMAGIC53D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: BY CCD FRAME
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: ANGULAR RECONSTITUTION FOLLOWED BY PROJECTION MATCHING
Resolution: 6.6 Å / Num. of particles: 70364 / Actual pixel size: 1.81 Å
Details: THIS ENTRY IS A MODEL OF THE METHANOTHERMOBACTER THERMAUTOTROPHICUS 50S-AIF6 COMPLEX AND WAS GENERATED BY RIGID BODY DOCKING OF HIGH RESOLUTION STRUCTURES INTO THE EXPERIMENTAL CRYO-EM MAP EMD-2012.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-ID
13CC2

3cc2

1
23O58

3o58
PDB Unreleased entry

1
34A17

4a17
PDB Unreleased entry

1
44A19

4a19
PDB Unreleased entry

1
RefinementHighest resolution: 6.6 Å
Refinement stepCycle: LAST / Highest resolution: 6.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 2942 0 0 7164

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