5IT7

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural characterization of ribosome recruitment and translocation by type IV IRES.

Murray, J.Savva, C.G.Shin, B.S.Dever, T.E.Ramakrishnan, V.Fernandez, I.S.

(2016) Elife 5

  • DOI: 10.7554/eLife.13567
  • Primary Citation of Related Structures:  
    5IT9, 5IT7

  • PubMed Abstract: 
  • Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the ...

    Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D16027p AA249Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CQM3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3 BB384Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CJR7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B07139p CC360Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CW41 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D06941p DD295Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRR9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B04686p EE170Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWE7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D03410p FF222Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CS71 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E00573p GG233Kluyveromyces lactisMutation(s): 0 
Find proteins for B4UN96 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F04499p HH191Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CLA6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D05643p II216Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRX7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F08261p JJ168Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CKT4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13 LL197Kluyveromyces lactisMutation(s): 0 
Find proteins for Q875M0 (Kluyveromyces lactis)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B13409p MM136Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CVB1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L15 NN202Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CJL7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F04675p OO198Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CL98 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0A06336p PP180Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CXQ6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0A07227p QQ184Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CXL8 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 20
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KLLA0E12453p RR188Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CNH9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20 SS169Kluyveromyces lactisMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E23651p TT158Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CM20 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D05181p UU100Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRZ8 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E06997p VV132Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CP75 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24 WW62Kluyveromyces lactisMutation(s): 0 
Find proteins for P38665 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25 XX121Kluyveromyces lactisMutation(s): 0 
Find proteins for P48045 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B05742p YY125Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CW97 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E03455p ZZ134Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CPN9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
RPL28 aa147Kluyveromyces lactisMutation(s): 0 
Find proteins for Q8J287 (Kluyveromyces lactis)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D16071p bb57Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CQM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30 cc97Kluyveromyces lactisMutation(s): 0 
Find proteins for P38664 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B02937p dd106Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWM6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E06843p ee122Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CP82 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D07405p ff105Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRP7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0C08371p gg121Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CU17 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F05247p hh116Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CL71 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 37
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60S ribosomal protein L36 ii98Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CR18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 38
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Ribosomal protein L37 jj85Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CUW0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 39
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KLLA0C18216p kk76Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CSS8 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39 ll49Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin fusion protein mm51Kluyveromyces lactisMutation(s): 0 
Gene Names: ubi1
Find proteins for Q9Y854 (Kluyveromyces lactis)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-A nn25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
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60S ribosomal protein L44 oo101Kluyveromyces lactisMutation(s): 0 
Find proteins for P31027 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 44
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KLLA0E05941p pp87Kluyveromyces lactisMutation(s): 0 
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Entity ID: 45
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Ribosomal protein qq217Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWR9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 46
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60S acidic ribosomal protein P0 rr195Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CW89 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 47
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uL11 KK147Kluyveromyces lactisMutation(s): 0 
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Entity ID: 48
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40S ribosomal protein S0 A206Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 49
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40S ribosomal protein S1 B214Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 50
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KLLA0F09812p C217Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CKL3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 51
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KLLA0D08305p D223Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 52
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40S ribosomal protein S4 E260Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 53
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KLLA0D10659p F206Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 54
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40S ribosomal protein S6 G226Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 55
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KLLA0C13519p H184Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CTD6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 56
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40S ribosomal protein S8 I200Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CMG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E23673p J182Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CM18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B08173p K96Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 59
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KLLA0A10483p L155Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 60
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40S ribosomal protein S12 M122Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 61
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KLLA0F18040p N150Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 62
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40S ribosomal protein S14 O127Kluyveromyces lactisMutation(s): 0 
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 63
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KLLA0F07843p P123Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CKV4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 64
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40S ribosomal protein S16 Q141Kluyveromyces lactisMutation(s): 0 
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B01474p R129Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B01562p S145Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 67
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KLLA0A07194p T143Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 68
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KLLA0F25542p U106Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CIM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 69
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40S ribosomal protein S21 V87Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 70
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40S ribosomal protein S22 W129Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 71
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RPS23 X145Kluyveromyces lactisMutation(s): 0 
Find proteins for Q875M3 (Kluyveromyces lactis)
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Entity ID: 72
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40S ribosomal protein S24 Y134Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 73
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KLLA0B06182p Z70Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CW78 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 74
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KLLA0D05115p a100Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 75
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40S ribosomal protein S27 b82Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 76
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40S ribosomal protein S28 c63Kluyveromyces lactisMutation(s): 0 
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 77
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40S ribosomal protein S29 d53Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 78
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KLLA0C04809p e55Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 79
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Ubiquitin-40S ribosomal protein S27a f69Kluyveromyces lactisMutation(s): 0 
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 80
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KLLA0E12277p g324Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 83
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Eft2p 1827Saccharomyces cerevisiae P283Mutation(s): 0 
Gene Names: Eft2P283_D20866
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Entity ID: 1
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25S ribosomal RNA53270Kluyveromyces lactis
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Entity ID: 2
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5S ribosomal RNA7121Kluyveromyces lactis
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Entity ID: 3
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5.8S ribosomal RNA8157Kluyveromyces lactis
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Entity ID: 81
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18S ribosomal RNA21798Kluyveromyces lactis
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Entity ID: 82
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cricket paralysis virus IRES4190Cricket paralysis virus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
1
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
6EM
Query on 6EM

Download Ideal Coordinates CCD File 
1
(2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium
C7 H17 N2 O
LPOFDMFKBRMZLU-LURJTMIESA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
a, b, f, jj, mm, oo
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
1, 2, 5, N, f
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
National Institutes of HealthUnited StatesIntramural Research Program

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-03-28
    Changes: Advisory
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations