5DC3

Complex of yeast 80S ribosome with non-modified eIF5A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome.

Melnikov, S., Mailliot, J., Shin, B.S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.

(2016) J Mol Biol 428: 3570-3576

  • DOI: 10.1016/j.jmb.2016.05.011
  • Primary Citation of Related Structures:  
    5DC3

  • PubMed Abstract: 

    • Eukaryotic translation initiation factor eIF5A promotes protein synthesis by resolving polyproline-induced ribosomal stalling. Here, we report a 3.25-Å resolution crystal structure of eIF5A bound to the yeast 80S ribosome. The structure reveals a previously unseen conformation of an eIF5A-ribosome complex and highlights a possible functional link between conformational changes of the ribosome during protein synthesis and the eIF5A-ribosome association ...

    Eukaryotic translation initiation factor eIF5A promotes protein synthesis by resolving polyproline-induced ribosomal stalling. Here, we report a 3.25-Å resolution crystal structure of eIF5A bound to the yeast 80S ribosome. The structure reveals a previously unseen conformation of an eIF5A-ribosome complex and highlights a possible functional link between conformational changes of the ribosome during protein synthesis and the eIF5A-ribosome association.

    Organizational Affiliation: 

    Université de Strasbourg, 4 Rue Blaise Pascal, 67081 Strasbourg, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-A S0, s0251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
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Entity ID: 3
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40S ribosomal protein S1-A S1, s1254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
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40S ribosomal protein S2 S2, s2253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3 S3, s3239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-A S4, s4260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5 S5, s5224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-A S6, s6236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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Entity ID: 9
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40S ribosomal protein S7-A S7, s7189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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Entity ID: 10
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40S ribosomal protein S8-A S8, s8200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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Entity ID: 11
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40S ribosomal protein S9-A S9, s9196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
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Entity ID: 12
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40S ribosomal protein S10-A C0105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10A, YOR293W
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Entity ID: 13
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40S ribosomal protein S11-A C1, c1155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 14
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40S ribosomal protein S12 C2, c2142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
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Entity ID: 15
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40S ribosomal protein S13 C3, c3150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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Entity ID: 16
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40S ribosomal protein S14-A C4, c4136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14A, CRY1, RPL59, YCR031C, YCR31C
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Entity ID: 17
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40S ribosomal protein S15 C5, c5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15, RPS21, YOL040C
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Entity ID: 18
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40S ribosomal protein S16-A C6, c6142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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Entity ID: 19
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40S ribosomal protein S17-A C7, c7136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17A, RP51A, YML024W
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Entity ID: 20
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40S ribosomal protein S18-A C8, c8145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
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Entity ID: 21
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40S ribosomal protein S19-A C9, c9143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19A, RP55A, RPS16AA, YOL121C
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Entity ID: 22
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40S ribosomal protein S20 D0, d0120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20, URP2, YHL015W
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Entity ID: 23
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40S ribosomal protein S21-A D1, d187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
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Entity ID: 24
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40S ribosomal protein S22-A D2, d2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-A D3, d3144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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Entity ID: 26
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40S ribosomal protein S24-A D4, d4134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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Entity ID: 27
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40S ribosomal protein S25-A D5, d5107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25A, RPS31A, YGR027C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-B D6, d697Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26B, YER131W
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
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40S ribosomal protein S27-A D7, d781Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
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40S ribosomal protein S28-A D8, d866Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
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Entity ID: 31
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40S ribosomal protein S29-A D9, d955Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29A, RPS36A, YS29A, YLR388W, L8084.11
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Entity ID: 32
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40S ribosomal protein S30-A E0, e062Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
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Entity ID: 33
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Ubiquitin-40S ribosomal protein S31 E1, e176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
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Entity ID: 34
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Guanine nucleotide-binding protein subunit beta-like protein SR, sR318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1, CPC2, YMR116C, YM9718.15C
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Entity ID: 35
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Suppressor protein STM1 SM, sM273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1, MPT4, STO1, YLR150W, L9634.1
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Entity ID: 39
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60S ribosomal protein L2-A L2, l2253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
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Entity ID: 40
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60S ribosomal protein L3 L3, l3386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
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Entity ID: 41
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60S ribosomal protein L4-A L4, l4361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
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Entity ID: 42
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60S ribosomal protein L5 L5, l5296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
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Entity ID: 43
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60S ribosomal protein L6-A L6, l6175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
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Entity ID: 44
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60S ribosomal protein L7-A L7, l7243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
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Entity ID: 45
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60S ribosomal protein L8-A L8, l8255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
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Entity ID: 46
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60S ribosomal protein L9-A L9, l9191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
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Entity ID: 47
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60S ribosomal protein L10 M0, m0220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10, GRC5, QSR1, YLR075W
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Entity ID: 48
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60S ribosomal protein L11-B M1, m1173Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11B, RP39B, RPL16B, YGR085C
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Entity ID: 49
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60S ribosomal protein L13-A M3, m3198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
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Entity ID: 50
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60S ribosomal protein L14-A M4, m4137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
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Entity ID: 51
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60S ribosomal protein L15-A M5, m5203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
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Entity ID: 52
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60S ribosomal protein L16-A M6, m6198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
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60S ribosomal protein L17-A M7, m7183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-A M8, m8185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
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Entity ID: 55
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60S ribosomal protein L19-A M9, m9188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
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Entity ID: 56
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60S ribosomal protein L20-A N0, n0172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
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Entity ID: 57
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60S ribosomal protein L21-A N1, n1159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
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Entity ID: 58
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60S ribosomal protein L22-A N2, n2120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 59
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60S ribosomal protein L23-A N3, n3136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
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Entity ID: 60
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60S ribosomal protein L24-A N4, n4155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24A, RP29, RPL30A, YGL031C
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Entity ID: 61
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60S ribosomal protein L25 N5, n5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
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Entity ID: 62
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60S ribosomal protein L26-A N6, n6126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
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Entity ID: 63
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60S ribosomal protein L27-A N7, n7135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
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Entity ID: 64
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60S ribosomal protein L28 N8, n8148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
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Entity ID: 65
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60S ribosomal protein L29 N9, n958Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29, YL43, YFR032C-A, YFR032BW
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30 O0, o0104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-A O1, o1112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
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Entity ID: 68
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60S ribosomal protein L32 O2, o2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
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Entity ID: 69
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60S ribosomal protein L33-A O3, o3106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-A O4, o4119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-A O5, o5119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-A O6, o699Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-A O7, o787Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38 O8, o877Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39 O9, o950Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40 Q0, q052Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-A Q1, q125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41A, RPL47A, YL41A, YDL184C, D1290
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-A Q2, q2105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42A, RPL41A, SCL41A, YNL162W, N1722
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Entity ID: 79
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60S ribosomal protein L43-A Q3, q391Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
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Entity ID: 80
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40S ribosomal protein S10-A c0105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 81
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60S ribosomal protein L12-A (uL11) m2150Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0 p0311Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8
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Entity ID: 83
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60S ribosomal protein P1 alpha p147Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 84
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60S ribosomal P2 beta p246Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 85
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Eukaryotic translation initiation factor 5A-1 f157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HYP2, TIF51A, YEL034W, SYGP-ORF21
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNA2, 61800Saccharomyces cerevisiae S288C
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Entity ID: 36
MoleculeChainsLengthOrganismImage
25S ribosomal RNA1, 53396Saccharomyces cerevisiae S288C
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Entity ID: 37
MoleculeChainsLengthOrganismImage
5S ribosomal RNA3, 7121Saccharomyces cerevisiae
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Entity ID: 38
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5.8S ribosomal RNA4, 8158Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 438.23α = 90
b = 289.33β = 98.95
c = 305.47γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFrance--
Austrian Science FundAustriaP21641
Austrian Science FundAustriaI1040
French National Research AgencyFranceANR-11-BSV8-006 01
European Research Council294312
Human Frontier Science ProgramRGP0062
Human Frontier Science ProgramRGP2012
Russian Government Program of Competitive Growh of Kazan Federal UniversityRussian Federation--
Intramural Research Program of the National Institutes of HealthUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Structure summary
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-02-20
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations