6GZ4

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



Literature

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J.Holm, M.Rundlet, E.J.Loerke, J.Hilal, T.Dabrowski, M.Burger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

(2018) Cell Rep 25: 2676-2688.e7

  • DOI: 10.1016/j.celrep.2018.11.040
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA subst ...

    Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA 2 ⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: tetyana.budkevych@charite.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL2
AA
252Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS2
BA
215Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS1
BB
212Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4
AC
363Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS28
BC
222Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS3
BD
220Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS7
BF
190Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS10
BK
98Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS12
BM
120Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS19
BP
120Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS9
BQ
139Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS17
BR
125Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS13
BS
139Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS19
BT
143Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS10
BU
97Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS10
BZ
86Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS28
Bc
62Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS14
Bd
51Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS31
Bf
73Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK 1
Bg
314Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS4
BE
257Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS6
BG
232Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS7
BH
183Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS8
BI
207Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS4
BJ
179Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS17
BL
153Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15
BN
149Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS11
BO
136Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS21
BV
81Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS8
BW
129Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS12
BX
141Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS24
BY
125Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS26
Ba
97Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS27
Bb
80Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS30
Be
55Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18
AD
294Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6
AE
194Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6
AH
191Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL16
AI
208Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL5
AJ
169Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13
AL
205Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14
AM
139Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL15
AN
203Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13
AO
195Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22
AP
153Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18
AQ
187Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19
AR
181Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20
AS
175Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21
AT
157Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22
AU
99Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL14
AV
129Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24
AW
121Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23
AX
117Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL24
AY
127Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL27
AZ
134Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15
Aa
147Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29
Ab
68Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30
Ac
103Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31
Ad
106Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32
Ae
129Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33
Af
109Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34
Ag
114Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29
Ah
122Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36
Ai
97Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38
Ak
69Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39
Al
50Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40
Am
50Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41
An
25Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43
Ap
91Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL1
Au
217Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL11
Aq
151Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
eukaryotic elongation factor 2 (eEF2)
Ct
853Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3
AB
394Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30
AF
234Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8
AG
234Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL37
Aj
84Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL42
Ao
105Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28
At
122Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL10
AK
202Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 9
MoleculeChainsLengthOrganism
mRNABx11Oryctolagus cuniculus

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Entity ID: 10
MoleculeChainsLengthOrganism
pe/E-site-tRNABw76Oryctolagus cuniculus

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Entity ID: 11
MoleculeChainsLengthOrganism
18S ribosomal RNAB11708Oryctolagus cuniculus

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Entity ID: 42
MoleculeChainsLengthOrganism
5.8S ribosomal RNAA3157Oryctolagus cuniculus

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Entity ID: 43
MoleculeChainsLengthOrganism
5S ribosomal RNAA4119Oryctolagus cuniculus

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Entity ID: 7
MoleculeChainsLengthOrganism
28S ribosomal RNAA23612Oryctolagus cuniculus

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Entity ID: 8
MoleculeChainsLengthOrganism
ap/P-site tRNABv76Oryctolagus cuniculus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
Ct
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
Aj, Ao, Ap, Ba, Bd
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A2, A3, A4, AA, AL, AY, An, B1, BD, BS, Ba, Bd, Bx
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
Ct
L-PEPTIDE LINKINGC13 H24 N5 O3HIS
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
German Research FoundationGermanyDFG SFB 740
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM115327-Tan

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 2.0: 2019-02-06
    Changes: Atomic model, Data collection, Derived calculations