ISDA

Deposition Date 2014-10-20

Release Date 2015-04-22

Last Version Date 2025-04-09

Entry Detail

PDB ID:

4V3P

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Triticum aestivum (Taxon ID: 4565)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

34.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SUBTOMOGRAM AVERAGING

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:26S ribosomal RNA
Chain IDs:GA (auth: L1)
Chain Length:3352
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:IA (auth: L2)
Chain Length:159
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:HA (auth: L3)
Chain Length:120
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Chain IDs:JA (auth: LA)
Chain Length:216
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L3 Pfam ID:PF00687

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Chain IDs:KA (auth: LB)
Chain Length:255
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L3
Gene (Uniprot):LOC123120076
Chain IDs:EC (auth: LC)
Chain Length:389
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q7X744 Pfam ID:PF00297

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4/L1
Chain IDs:FC (auth: LD)
Chain Length:372
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Chain IDs:LA (auth: LE)
Chain Length:244
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L2 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Chain IDs:MA (auth: LF)
Chain Length:112
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:LB (auth: LG)
Chain Length:120
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L4 Pfam ID:PF01159

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Chain IDs:NA (auth: LH)
Chain Length:133
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10-1
Chain IDs:IC (auth: LI)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Chain IDs:WB (auth: LJ)
Chain Length:104
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13a
Chain IDs:GC (auth: LK)
Chain Length:77
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L1 Pfam ID:PF00572

Polymer Type:polypeptide(L)
Molecule:Unknown 60S wheat germ ribosome protein 5
Chain IDs:MB (auth: LL)
Chain Length:182
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal Pr 117
Chain IDs:OA (auth: LM)
Chain Length:140
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K4 Pfam ID:PF00238

Polymer Type:polypeptide(L)
Molecule:Unknown 60S wheat germ ribosome protein 6
Chain IDs:NB (auth: LN)
Chain Length:69
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a-3
Chain IDs:QA (auth: LO)
Chain Length:144
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Chain IDs:PA (auth: LP)
Chain Length:41
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:SA (auth: LQ)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:RA (auth: LR)
Chain Length:163
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L0 Pfam ID:PF17135

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Chain IDs:OB (auth: LS)
Chain Length:262
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19
Chain IDs:TA (auth: LT)
Chain Length:58
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q7XY20 Pfam ID:PF01280

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Chain IDs:UA (auth: LU)
Chain Length:58
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Chain IDs:VA (auth: LV)
Chain Length:59
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Chain IDs:PB (auth: LW)
Chain Length:59
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Chain IDs:WA (auth: LX)
Chain Length:122
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Chain IDs:YA (auth: LY)
Chain Length:20
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Chain IDs:XA (auth: LZ)
Chain Length:75
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:QB (auth: La)
Chain Length:216
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l28
Chain IDs:ZA (auth: Lb)
Chain Length:255
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:BC (auth: Lc)
Chain Length:389
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L805 Pfam ID:PF00831

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:AB (auth: Ld)
Chain Length:372
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L7
Chain IDs:CC (auth: Le)
Chain Length:244
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K6 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Chain IDs:BB (auth: Lf)
Chain Length:112
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K9 Pfam ID:PF01248

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Chain IDs:CB (auth: Lg)
Chain Length:120
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Ribosomal L32
Chain IDs:DB (auth: Lh)
Chain Length:133
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein l34
Chain IDs:RB (auth: Li)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K8 Pfam ID:PF01199

Polymer Type:polypeptide(L)
Molecule:ribosomal protein L35A
Chain IDs:SB (auth: Lj)
Chain Length:104
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Chain IDs:TB (auth: Lk)
Chain Length:77
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A9R1H1R6

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Chain IDs:EB (auth: Ll)
Chain Length:182
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a, expressed
Gene (Uniprot):TAA_ctg0616b.00240.1, TRAES_3BF073800030CFD_c1
Chain IDs:HC (auth: Lm)
Chain Length:140
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:D8L9P6 Pfam ID:PF01780

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Chain IDs:FB (auth: Ln)
Chain Length:69
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L39
Gene (Uniprot):LOC123167131
Chain IDs:GB (auth: Lo)
Chain Length:144
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K7 Pfam ID:PF00832

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40-1
Chain IDs:UB (auth: Lp)
Chain Length:41
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Unknown 60S wheat germ ribosome protein 1
Chain IDs:IB (auth: Lq)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L44
Chain IDs:HB (auth: Lr)
Chain Length:163
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:DC (auth: Ls)
Chain Length:262
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein P1
Gene (Uniprot):LOC606341
Chain IDs:XB (auth: Lt), YB (auth: Lu)
Chain Length:58
Number of Molecules:2
Biological Source:Triticum aestivum

UniProt ID:Q5I7K5 Pfam ID:PF00428

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P2A
Chain IDs:ZB (auth: Lv), AC (auth: Lw)
Chain Length:59
Number of Molecules:2
Biological Source:Triticum aestivum

UniProt ID:W5AP46 Pfam ID:PF00428

Polymer Type:polypeptide(L)
Molecule:Unknown 60S wheat germ ribosome protein 2
Chain IDs:JB (auth: Ly), VB (auth: Lx)
Chain Length:122
Number of Molecules:2
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Unknown 60S wheat germ ribosome protein 3
Chain IDs:KB (auth: Lz)
Chain Length:75
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:FA (auth: S1)
Chain Length:1743
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:40S ribosomal RNA
Chain IDs:EA (auth: S2)
Chain Length:75
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:40S WHEAT GERM RIBOSOME protein 4
Chain IDs:DA (auth: S3)
Chain Length:11
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Chain IDs:B (auth: SA)
Chain Length:260
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 40S ribosomal protein S3
Chain IDs:C (auth: SB)
Chain Length:36
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L804 Pfam ID:PF07650, PF00189

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Chain IDs:Y (auth: SC)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Chain IDs:D (auth: SD)
Chain Length:200
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:E (auth: SE)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Chain IDs:F (auth: SF)
Chain Length:191
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Unknown 40S wheat germ ribosome protein 4
Chain IDs:Z (auth: SG)
Chain Length:143
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15
Chain IDs:AA (auth: SH)
Chain Length:130
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Chain IDs:G (auth: SI)
Chain Length:126
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Chain IDs:H (auth: SJ)
Chain Length:128
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Chain IDs:I (auth: SK)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:J (auth: SL)
Chain Length:142
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Chain IDs:K (auth: SM)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:BA (auth: SN)
Chain Length:48
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K3 Pfam ID:PF00253

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13-1
Chain IDs:L (auth: SO)
Chain Length:121
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:N (auth: SP)
Chain Length:85
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-4
Chain IDs:M (auth: SQ)
Chain Length:141
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:P (auth: SR)
Chain Length:91
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Chain IDs:O (auth: SS)
Chain Length:146
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:CA (auth: ST)
Chain Length:82
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Unknown 40S wheat germ ribosome protein 3
Chain IDs:W (auth: SU)
Chain Length:98
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:Q (auth: SV)
Chain Length:100
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S WHEAT GERM RIBOSOME1
Chain IDs:R (auth: SW)
Chain Length:92
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:X (auth: SX)
Chain Length:50
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Chain IDs:S (auth: SY)
Chain Length:58
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:T (auth: SZ)
Chain Length:62
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:G protein beta subunit
Gene (Uniprot):TaGB1
Chain IDs:A (auth: Sa)
Chain Length:260
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8LNY6 Pfam ID:PF00400

Polymer Type:polypeptide(L)
Molecule:Unknown 40S wheat germ ribosome protein 3
Chain IDs:V (auth: Sb)
Chain Length:36
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Unknown 40S wheat germ ribosome protein 2
Chain IDs:U (auth: Sc)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Ligand Molecules

Primary Citation

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.Show

Nat Commun 5 5294 5294 (2014)

PMID: 25376914 DOI: 10.1038/ncomms6294

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures