4V4B

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

Spahn, C.M.Gomez-Lorenzo, M.G.Grassucci, R.A.Jorgensen, R.Andersen, G.R.Beckmann, R.Penczek, P.A.Ballesta, J.P.Frank, J.

(2004) Embo J. 23: 1008-1019

  • DOI: 10.1038/sj.emboj.7600102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the fu ...

    An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.


    Related Citations: 
    • The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery.
      Ballesta, J.P.,Remacha, M.
      (1996) PROG.NUCLEIC ACID RES.MOL.BIOL. 55: 157
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
      Ban, N.,Nissen, P.,Hansen, J.,Moore, P.B.,Steitz, T.A.
      (2000) Science 289: 905
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
      Agrawal, R.K.,Heagle, A.B.,Penczek, P.,Grassucci, R.A.,Frank, J.
      (1999) Nat.Struct.Mol.Biol. 6: 643


    Organizational Affiliation

    Wadsworth Center, Health Research Inc., Howard Hughes Medical Institute, Albany, NY 12201-0509, USA. christian.spahn@charite.de




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 2
AT
842Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EFT1, EFT2
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32324
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
AB
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
AC
192Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05750
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
AD
179Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
AE
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2
Go to UniProtKB:  P25443
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
AG
150Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS5
Go to UniProtKB:  P26783
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22
AH
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
AI
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
AJ
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38701
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
AK
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
AL
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23B (RPS28B)
Find proteins for P0CX30 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX30
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
AM
132Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS18B
Find proteins for P0CX56 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX56
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-B
AN
36Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS29B (RPS36B, YS29B)
Find proteins for P41058 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41058
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
AO
65Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS13
Go to UniProtKB:  P05756
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
AQ
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
AS
80Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS15
Go to UniProtKB:  Q01855
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1
BA
217Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL1A (SSM1, SSM1A)
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX43
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
BB
253Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
BC
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P14126
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-B
BD
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4B (RPL2B)
Find proteins for P49626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49626
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
BE
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P26321
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
BF
162Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
BG
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
BH
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
BI
168Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
BJ
173Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11A (RP39A, RPL16A)
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12
BK
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL12A (RPL15B)
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX53
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
BL
203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
BM
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
BN
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
BO
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18B (RP28B)
Find proteins for P0CX50 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX50
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
BP
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19B (RPL23B, YL14B)
Find proteins for P0CX83 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX83
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
BQ
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
BR
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23B (RPL17AB, RPL17B)
Find proteins for P0CX42 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX42
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
BS
56Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
BT
83Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
BU
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
BV
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
B0
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31
BW
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31B (RPL34, RPL34B)
Find proteins for P0C2H9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H9
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
BX
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
BY
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42
BZ
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43
B9
91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43B
Find proteins for P0CX26 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX26
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAAA1507Saccharomyces cerevisiae
Entity ID: 18
MoleculeChainsLengthOrganism
5.8S/25S ribosomal RNAB32999Saccharomyces cerevisiae
Entity ID: 19
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAB4125Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-03-18
    Type: Other