6GZ3

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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.Buerger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS3
BD
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S5
BF
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
Go to Gene View: RPS5
Go to UniProtKB:  G1TFM5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS10
BK
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TPV3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
BM
120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
Go to Gene View: RPS12
Go to UniProtKB:  G1SFR8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS19
BP
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS9
BQ
139N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS17
BR
125Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
Go to Gene View: RPS17
Go to UniProtKB:  G1TU13
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS13
BS
139Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356144
Find proteins for G1TPG3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TPG3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS19
BT
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS10
BU
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25
BZ
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS25
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Go to Gene View: RPS25
Go to UniProtKB:  G1TDB3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S28
Bc
62Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TIB4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS14
Bd
51Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS29
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to Gene View: RPS29
Go to UniProtKB:  G1U7M4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S27a
Bf
73Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348379
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SK22
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK 1
Bg
314Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to Gene View: RACK1
Go to UniProtKB:  G1SJB4
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS2
BA
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
BB
212Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A (LOC100342838, LOC100348981)
Find proteins for G1SS70 (Oryctolagus cuniculus)
Go to Gene View: RPS3A
Go to UniProtKB:  G1SS70
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS5
BC
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS4
BE
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
BG
232Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS6 (LOC108178879)
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to Gene View: RPS6
Go to UniProtKB:  G1TM55
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
BH
183Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS7
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Go to Gene View: RPS7
Go to UniProtKB:  G1SVB0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS8
BI
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S9 (Predicted)
BJ
179Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
Go to Gene View: RPS9
Go to UniProtKB:  B7NZS8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S11
BL
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
Find proteins for G1TRM4 (Oryctolagus cuniculus)
Go to Gene View: RPS11
Go to UniProtKB:  G1TRM4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15
BN
149Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to Gene View: RPS13
Go to UniProtKB:  G1SP51
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS11
BO
136N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS21
BV
81N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15a
BW
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
Go to Gene View: RPS15A
Go to UniProtKB:  G1TG89
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S23
BX
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
Go to Gene View: RPS23
Go to UniProtKB:  G1SZ47
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS24
BY
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS26
Ba
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS27
Bb
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS30
Be
55N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L8
AA
252Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL8
Find proteins for G1TT27 (Oryctolagus cuniculus)
Go to Gene View: RPL8
Go to UniProtKB:  G1TT27
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3
AB
394N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4
AC
363N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18
AD
294N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6
AE
194N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30
AF
234N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8
AG
234N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6
AH
191N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)
AI
211Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
Go to Gene View: RPL10
Go to UniProtKB:  B7NZQ2
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11
AJ
169Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL11
Find proteins for G1TUB8 (Oryctolagus cuniculus)
Go to Gene View: RPL11
Go to UniProtKB:  G1TUB8
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13
AL
205N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14
AM
139N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
AN
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15 (LOC100358370)
Find proteins for G1T0C1 (Oryctolagus cuniculus)
Go to Gene View: RPL15
Go to UniProtKB:  G1T0C1
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13
AO
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22
AP
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18
AQ
187N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19
AR
181N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20
AS
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21
AT
157Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108175794 (LOC108178019)
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SHQ2
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22
AU
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23
AV
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351949
Find proteins for G1T6D1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T6D1
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24
AW
121Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
Go to Gene View: RPL24
Go to UniProtKB:  G1SE28
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23
AX
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26
AY
127Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
Go to Gene View: RPL26
Go to UniProtKB:  G1SQH0
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
AZ
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974 (RPL27)
Find proteins for G1TXF6 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TXF6
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15
Aa
147N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29
Ab
68N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30
Ac
103N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31
Ad
106Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
Go to Gene View: RPL31
Go to UniProtKB:  G1SHG0
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32
Ae
129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUN8 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TUN8
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33
Af
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34
Ag
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29
Ah
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36
Ai
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
Aj
84Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
Go to Gene View: RPL37
Go to UniProtKB:  U3KPD5
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38
Ak
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39
Al
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108178831
Find proteins for G1SYU7 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SYU7
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40
Am
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41
An
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL42
Ao
105Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T040
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43
Ap
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807
Find proteins for G1SY53 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SY53
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28
At
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein
Au
217Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10A
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
Go to Gene View: RPL10A
Go to UniProtKB:  G1SKZ8
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12
Aq
151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
Go to Gene View: RPL12
Go to UniProtKB:  G1SMR7
Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL10
AK
202N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
eukaryotic elongation factor 2 (eEF2)
Ct
853N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNAA23612Oryctolagus cuniculus
Entity ID: 2
MoleculeChainsLengthOrganism
ap/P-site tRNABv76Oryctolagus cuniculus
Entity ID: 3
MoleculeChainsLengthOrganism
mRNABx12Salmonella virus SP6
Entity ID: 4
MoleculeChainsLengthOrganism
pe/E-site-tRNABw76Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
18S ribosomal RNAB11708Oryctolagus cuniculus
Entity ID: 39
MoleculeChainsLengthOrganism
5.8S ribosomal RNAA3157Oryctolagus cuniculus
Entity ID: 40
MoleculeChainsLengthOrganism
5S ribosomal RNAA4119Oryctolagus cuniculus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A2, A3, A4, AA, Al, AL, An, AN, AP, AY, B1, Ba, BD, Bd, BS, Bx
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
Ct
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-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: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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