4V3P

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report


This is version 1.7 of the entry. See complete history

Literature

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov, A.G.Afonina, Z.A.Menetret, J.F.Shirokov, V.A.Spirin, A.S.Klaholz, B.P.

(2014) Nat Commun 5: 5294-5294

  • DOI: 10.1038/ncomms6294

  • PubMed Abstract: 
  • During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from ...

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.


    Organizational Affiliation

    1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France.,Institute of Protein Research, Russian Academy of Sciences, 142290 Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G protein beta subunit
Sa
380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
Find proteins for Q8LNY6 (Triticum aestivum)
Go to UniProtKB:  Q8LNY6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
SA
260N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Putative 40S ribosomal protein S3
SB
208Triticum aestivumMutation(s): 0 
Find proteins for Q8L804 (Triticum aestivum)
Go to UniProtKB:  Q8L804
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
SD
200N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
SE
263N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
SF
191N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
SI
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
SJ
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
SK
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
SL
142N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
SM
152N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13-1
SO
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-4
SQ
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
SP
85N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
SS
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
SR
91N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
SV
100N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S WHEAT GERM RIBOSOME1
SW
92N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
SY
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
SZ
62N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 2
Sc
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 3
Sb
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 3
SU
98N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
SX
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
SC
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 4
SG
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15
SH
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
SN
48Triticum aestivumMutation(s): 0 
Gene Names: RPS29
Find proteins for Q5I7K3 (Triticum aestivum)
Go to Gene View: RPS29
Go to UniProtKB:  Q5I7K3
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
ST
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein
LA
216Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L3 (Triticum aestivum)
Go to UniProtKB:  Q5I7L3
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
LB
255N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11
LE
170Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L2 (Triticum aestivum)
Go to UniProtKB:  Q5I7L2
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9
LF
190N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7a
LH
201N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Pr 117
LM
140Triticum aestivumMutation(s): 0 
Find proteins for Q7X9K1 (Triticum aestivum)
Go to UniProtKB:  Q7X9K1
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
LP
194N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27a-3
LO
144N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
LR
163Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L0 (Triticum aestivum)
Go to UniProtKB:  Q5I7L0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
LQ
304N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L19
LT
189Triticum aestivumMutation(s): 0 
Find proteins for Q7XY20 (Triticum aestivum)
Go to UniProtKB:  Q7XY20
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21
LU
164N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17
LV
171N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23a
LX
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24
LZ
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26
LY
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein l28
Lb
73N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
Ld
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
Lf
112Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K9 (Triticum aestivum)
Go to UniProtKB:  Q5I7K9
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31
Lg
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Ribosomal L32
Lh
133N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
Ll
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
Ln
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L39
Lo
51Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K7 (Triticum aestivum)
Go to UniProtKB:  Q5I7K7
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44
Lr
105N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 1
Lq
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 2
Ly, Lx
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 3
Lz
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
LG
219Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L4 (Triticum aestivum)
Go to UniProtKB:  Q5I7L4
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 5
LL
182N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 6
LN
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
LS
167N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
LW
108N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
La
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein l34
Li
119Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K8 (Triticum aestivum)
Go to UniProtKB:  Q5I7K8
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L35A
Lj
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
Lk
77Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L5 (Triticum aestivum)
Go to UniProtKB:  Q5I7L5
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40-1
Lp
41N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12
LJ
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein P1
Lt, Lu
58Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K5 (Triticum aestivum)
Go to UniProtKB:  Q5I7K5
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P2A
Lv, Lw
59Triticum aestivumMutation(s): 0 
Find proteins for W5AP46 (Triticum aestivum)
Go to UniProtKB:  W5AP46
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
Lc
124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
Find proteins for Q8L805 (Triticum aestivum)
Go to Gene View: RPL35
Go to UniProtKB:  Q8L805
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7
Le
244Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K6 (Triticum aestivum)
Go to UniProtKB:  Q5I7K6
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
Ls
262N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L3
LC
389Triticum aestivumMutation(s): 0 
Gene Names: RPL3 (RPL3-A1, RPL3A-1)
Find proteins for Q7X744 (Triticum aestivum)
Go to Gene View: RPL3
Go to UniProtKB:  Q7X744
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4/L1
LD
372N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13a
LK
206Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L1 (Triticum aestivum)
Go to UniProtKB:  Q5I7L1
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a, expressed
Lm
92Triticum aestivumMutation(s): 0 
Find proteins for D8L9P6 (Triticum aestivum)
Go to UniProtKB:  D8L9P6
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10-1
LI
184N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsLengthOrganism
40S WHEAT GERM RIBOSOME protein 4S311Triticum aestivum
Entity ID: 31
MoleculeChainsLengthOrganism
40S ribosomal RNAS275Triticum aestivum
Entity ID: 32
MoleculeChainsLengthOrganism
18S ribosomal RNAS11743Triticum aestivum
Entity ID: 33
MoleculeChainsLengthOrganism
26S ribosomal RNAL13352Triticum aestivum
Entity ID: 34
MoleculeChainsLengthOrganism
5S ribosomal RNAL3120Triticum aestivum
Entity ID: 35
MoleculeChainsLengthOrganism
5.8S ribosomal RNAL2159Triticum aestivum
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
LL, Lx, Ly, Lz, Sb, Sc, SG, SW
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Atomic model
  • Version 1.2: 2017-06-28
    Type: Data collection, Refinement description, Structure summary
  • Version 1.3: 2017-07-26
    Type: Database references, Structure summary
  • Version 1.4: 2017-08-23
    Type: Data collection, Derived calculations
  • Version 1.5: 2018-06-20
    Type: Advisory, Data collection, Database references, Derived calculations
  • Version 1.6: 2018-10-24
    Type: Advisory, Data collection, Derived calculations
  • Version 1.7: 2018-11-21
    Type: Advisory, Data collection, Derived calculations