4V3P

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 34.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.8 of the entry. See complete history


Literature

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov, A.G.Afonina, Z.A.Menetret, J.F.Shirokov, V.A.Spirin, A.S.Klaholz, B.P.

(2014) Nat Commun 5: 5294-5294

  • DOI: 10.1038/ncomms6294
  • Primary Citation of Related Structures:  
    4V3P

  • PubMed Abstract: 
  • During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting ...

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.


    Organizational Affiliation

    1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
G protein beta subunitA [auth Sa]380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
UniProt
Find proteins for Q8LNY6 (Triticum aestivum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth SA]260Triticum aestivumMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3C [auth SB]208Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q8L804 (Triticum aestivum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4D [auth SD]200Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2E [auth SE]263Triticum aestivumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SF]191Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16G [auth SI]126Triticum aestivumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20H [auth SJ]128Triticum aestivumMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14I [auth SK]119Triticum aestivumMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23J [auth SL]142Triticum aestivumMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18K [auth SM]152Triticum aestivumMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13-1L [auth SO]121Triticum aestivumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-4M [auth SQ]141Triticum aestivumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11N [auth SP]85Triticum aestivumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19O [auth SS]146Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15P [auth SR]91Triticum aestivumMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25Q [auth SV]100Triticum aestivumMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S WHEAT GERM RIBOSOME1R [auth SW]92Triticum aestivumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28S [auth SY]58Triticum aestivumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30T [auth SZ]62Triticum aestivumMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 40S wheat germ ribosome protein 2U [auth Sc]25Triticum aestivumMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 40S wheat germ ribosome protein 3V [auth Sb]36Triticum aestivumMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 40S wheat germ ribosome protein 3W [auth SU]98Triticum aestivumMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27X [auth SX]50Triticum aestivumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9Y [auth SC]195Triticum aestivumMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 40S wheat germ ribosome protein 4Z [auth SG]143Triticum aestivumMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15AA [auth SH]130Triticum aestivumMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29BA [auth SN]48Triticum aestivumMutation(s): 0 
Gene Names: RPS29
UniProt
Find proteins for Q5I7K3 (Triticum aestivum)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21CA [auth ST]82Triticum aestivumMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinJA [auth LA]216Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2KA [auth LB]255Triticum aestivumMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11LA [auth LE]170Triticum aestivumMutation(s): 0 
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Find proteins for Q5I7L2 (Triticum aestivum)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9MA [auth LF]190Triticum aestivumMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7aNA [auth LH]201Triticum aestivumMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal Pr 117OA [auth LM]140Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L15PA [auth LP]194Triticum aestivumMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27a-3QA [auth LO]144Triticum aestivumMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18RA [auth LR]163Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q5I7L0 (Triticum aestivum)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5SA [auth LQ]304Triticum aestivumMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L19TA [auth LT]189Triticum aestivumMutation(s): 1 
UniProt
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21UA [auth LU]164Triticum aestivumMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17VA [auth LV]171Triticum aestivumMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23aWA [auth LX]122Triticum aestivumMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24XA [auth LZ]75Triticum aestivumMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26YA [auth LY]130Triticum aestivumMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein l28ZA [auth Lb]73Triticum aestivumMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29AB [auth Ld]23Triticum aestivumMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30BB [auth Lf]112Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q5I7K9 (Triticum aestivum)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31CB [auth Lg]120Triticum aestivumMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal L32DB [auth Lh]133Triticum aestivumMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37EB [auth Ll]94Triticum aestivumMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38FB [auth Ln]69Triticum aestivumMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L39GB [auth Lo]51Triticum aestivumMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L44HB [auth Lr]105Triticum aestivumMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 60S wheat germ ribosome protein 1IB [auth Lq]25Triticum aestivumMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 60S wheat germ ribosome protein 2VB [auth Lx], JB [auth Ly]20Triticum aestivumMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 60S wheat germ ribosome protein 3KB [auth Lz]14Triticum aestivumMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6LB [auth LG]219Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 60S wheat germ ribosome protein 5MB [auth LL]182Triticum aestivumMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown 60S wheat germ ribosome protein 6NB [auth LN]134Triticum aestivumMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18aOB [auth LS]167Triticum aestivumMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22PB [auth LW]108Triticum aestivumMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27QB [auth La]99Triticum aestivumMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein l34RB [auth Li]119Triticum aestivumMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein L35ASB [auth Lj]104Triticum aestivumMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36TB [auth Lk]77Triticum aestivumMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40-1UB [auth Lp]41Triticum aestivumMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L12WB [auth LJ]128Triticum aestivumMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein P1XB [auth Lt], YB [auth Lu]58Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P2AZB [auth Lv], AC [auth Lw]59Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35BC [auth Lc]124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
UniProt
Find proteins for Q8L805 (Triticum aestivum)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L7CC [auth Le]244Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q5I7K6 (Triticum aestivum)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0DC [auth Ls]262Triticum aestivumMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L3EC [auth LC]389Triticum aestivumMutation(s): 0 
Gene Names: RPL3RPL3-A1RPL3A-1
UniProt
Find proteins for Q7X744 (Triticum aestivum)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4/L1FC [auth LD]372Triticum aestivumMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L13aGC [auth LK]206Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q5I7L1 (Triticum aestivum)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37a, expressedHC [auth Lm]92Triticum aestivumMutation(s): 0 
Gene Names: TAA_ctg0616b.00240.1TRAES_3BF073800030CFD_c1
UniProt
Find proteins for D8L9P6 (Triticum aestivum)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10-1IC [auth LI]184Triticum aestivumMutation(s): 0 
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  • Entity ID: 30
    MoleculeChainsLengthOrganismImage
    40S WHEAT GERM RIBOSOME protein 4DA [auth S3]11Triticum aestivum
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    Entity ID: 31
    MoleculeChainsLengthOrganismImage
    40S ribosomal RNAEA [auth S2]75Triticum aestivum
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    Entity ID: 32
    MoleculeChainsLengthOrganismImage
    18S ribosomal RNAFA [auth S1]1743Triticum aestivum
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    Entity ID: 33
    MoleculeChainsLengthOrganismImage
    26S ribosomal RNAGA [auth L1]3352Triticum aestivum
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    Entity ID: 34
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAHA [auth L3]120Triticum aestivum
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 35
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAIA [auth L2]159Triticum aestivum
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 34.0 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SUBTOMOGRAM AVERAGING 

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-04-22
      Type: Initial release
    • Version 1.1: 2016-12-14
      Changes: Atomic model
    • Version 1.2: 2017-06-28
      Changes: Data collection, Refinement description, Structure summary
    • Version 1.3: 2017-07-26
      Changes: Database references, Structure summary
    • Version 1.4: 2017-08-23
      Changes: Data collection, Derived calculations
    • Version 1.5: 2018-06-20
      Changes: Advisory, Data collection, Database references, Derived calculations
    • Version 1.6: 2018-10-24
      Changes: Advisory, Data collection, Derived calculations
    • Version 1.7: 2018-11-21
      Changes: Advisory, Data collection, Derived calculations
    • Version 1.8: 2019-12-18
      Changes: Other