ISDA

Deposition Date 2020-06-27

Release Date 2020-10-07

Last Version Date 2024-04-24

Entry Detail

PDB ID:

6ZJ3

Keywords:

RIBOSOME

Title:

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis

Biological Source:

Source Organism:

Euglena gracilis (Taxon ID: 3039)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.15 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL39
Chain IDs:NC (auth: L1)
Chain Length:51
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL40
Chain IDs:OC (auth: L2)
Chain Length:126
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL41
Chain IDs:PC (auth: L3)
Chain Length:34
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL43
Chain IDs:RC (auth: L4)
Chain Length:106
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL42
Chain IDs:QC (auth: L5)
Chain Length:92
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eLEgr2
Chain IDs:SC (auth: L6)
Chain Length:69
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eLEgr3
Chain IDs:TC (auth: L7)
Chain Length:64
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:NA (auth: LA)
Chain Length:163
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 1
Chain IDs:OA (auth: LB)
Chain Length:204
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 2
Chain IDs:PA (auth: LC)
Chain Length:215
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 3
Chain IDs:QA (auth: LD)
Chain Length:260
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 4
Chain IDs:RA (auth: LE)
Chain Length:698
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 5
Chain IDs:SA (auth: LF)
Chain Length:250
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 6
Chain IDs:TA (auth: LG)
Chain Length:234
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 7
Chain IDs:UA (auth: LH)
Chain Length:159
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 8
Chain IDs:VA (auth: LI)
Chain Length:164
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 9
Chain IDs:WA (auth: LJ)
Chain Length:170
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 10
Chain IDs:XA (auth: LK)
Chain Length:64
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 11
Chain IDs:YA (auth: LL)
Chain Length:95
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 12
Chain IDs:ZA (auth: LM)
Chain Length:157
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:LSU rRNA chain 13
Chain IDs:AB (auth: LN)
Chain Length:134
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:BB (auth: LO)
Chain Length:72
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL2
Chain IDs:CB (auth: LP)
Chain Length:123
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL3
Chain IDs:DB (auth: LQ)
Chain Length:410
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL4
Chain IDs:EB (auth: LR)
Chain Length:375
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL5
Chain IDs:FB (auth: LS)
Chain Length:191
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL6
Chain IDs:GB (auth: LT)
Chain Length:193
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL6
Chain IDs:HB (auth: LU)
Chain Length:139
Number of Molecules:1
Biological Source:Euglena gracilis

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Chain IDs:IB (auth: LV)
Chain Length:295
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:Q4VH13 Pfam ID:PF01248

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL13
Chain IDs:JB (auth: LW)
Chain Length:128
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL13
Chain IDs:KB (auth: LX)
Chain Length:226
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL14
Chain IDs:LB (auth: LY)
Chain Length:117
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL14
Chain IDs:MB (auth: LZ)
Chain Length:219
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL15
Chain IDs:NB (auth: La)
Chain Length:163
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL15
Chain IDs:OB (auth: Lb)
Chain Length:204
Number of Molecules:1
Biological Source:Euglena gracilis

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:PB (auth: Lc)
Chain Length:215
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:Q39724 Pfam ID:PF00252

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL18
Chain IDs:QB (auth: Ld)
Chain Length:260
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL18
Chain IDs:RB (auth: Le)
Chain Length:698
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL19
Chain IDs:SB (auth: Lf)
Chain Length:250
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL20
Chain IDs:TB (auth: Lg)
Chain Length:234
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL21
Chain IDs:UB (auth: Lh)
Chain Length:159
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL22
Chain IDs:VB (auth: Li)
Chain Length:164
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL22
Chain IDs:WB (auth: Lj)
Chain Length:170
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL23
Chain IDs:XB (auth: Lk)
Chain Length:64
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL24
Chain IDs:YB (auth: Ll)
Chain Length:95
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL24
Chain IDs:ZB (auth: Lm)
Chain Length:157
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL27
Chain IDs:AC (auth: Ln)
Chain Length:134
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eLEgr1
Chain IDs:BC (auth: Lo)
Chain Length:72
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL29
Chain IDs:CC (auth: Lp)
Chain Length:123
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL29
Chain IDs:DC (auth: Lq)
Chain Length:410
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL30
Chain IDs:EC (auth: Lr)
Chain Length:375
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL30
Chain IDs:FC (auth: Ls)
Chain Length:191
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL31
Chain IDs:GC (auth: Lt)
Chain Length:193
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL32
Chain IDs:HC (auth: Lu)
Chain Length:139
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL33
Chain IDs:IC (auth: Lv)
Chain Length:295
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL34
Chain IDs:JC (auth: Lw)
Chain Length:128
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL36
Chain IDs:KC (auth: Lx)
Chain Length:226
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL37
Chain IDs:LC (auth: Ly)
Chain Length:117
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL38
Chain IDs:MC (auth: Lz)
Chain Length:219
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: S1)
Chain Length:2315
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:A-tRNA
Chain IDs:B (auth: S2)
Chain Length:76
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:P-tRNA
Chain IDs:C (auth: S3)
Chain Length:76
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:E-tRNA
Chain IDs:D (auth: S4)
Chain Length:76
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:E (auth: S5)
Chain Length:12
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS1
Chain IDs:F (auth: SA)
Chain Length:249
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS2
Chain IDs:G (auth: SB)
Chain Length:120
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS3
Chain IDs:H (auth: SC)
Chain Length:86
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS4
Chain IDs:I (auth: SD)
Chain Length:76
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS4
Chain IDs:J (auth: SE)
Chain Length:67
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS5
Chain IDs:K (auth: SF)
Chain Length:257
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS6
Chain IDs:L (auth: SG)
Chain Length:283
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS7
Chain IDs:M (auth: SH)
Chain Length:190
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS7
Chain IDs:N (auth: SI)
Chain Length:200
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS8
Chain IDs:O (auth: SJ)
Chain Length:130
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS8
Chain IDs:P (auth: SK)
Chain Length:304
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS9
Chain IDs:Q (auth: SL)
Chain Length:151
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS10
Chain IDs:R (auth: SM)
Chain Length:121
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS10
Chain IDs:S (auth: SN)
Chain Length:152
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS11
Chain IDs:T (auth: SO)
Chain Length:152
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS12
Chain IDs:U (auth: SP)
Chain Length:143
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS12
Chain IDs:V (auth: SQ)
Chain Length:139
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS13
Chain IDs:W (auth: SR)
Chain Length:153
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS14
Chain IDs:X (auth: SS)
Chain Length:55
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS15
Chain IDs:Y (auth: ST)
Chain Length:151
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS17
Chain IDs:Z (auth: SU)
Chain Length:164
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS17
Chain IDs:AA (auth: SV)
Chain Length:145
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS19
Chain IDs:BA (auth: SW)
Chain Length:150
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS19
Chain IDs:CA (auth: SX)
Chain Length:148
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS21
Chain IDs:DA (auth: SY)
Chain Length:96
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS24
Chain IDs:EA (auth: SZ)
Chain Length:137
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS25
Chain IDs:FA (auth: Sa)
Chain Length:249
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS26
Chain IDs:GA (auth: Sb)
Chain Length:120
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS27
Chain IDs:HA (auth: Sc)
Chain Length:86
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS28
Chain IDs:IA (auth: Sd)
Chain Length:76
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS30
Chain IDs:JA (auth: Se)
Chain Length:67
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS31
Chain IDs:KA (auth: Sf)
Chain Length:257
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eSEug1
Chain IDs:LA (auth: Sg)
Chain Length:283
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:RACK1
Chain IDs:MA (auth: Sh)
Chain Length:190
Number of Molecules:1
Biological Source:Euglena gracilis

Ligand Molecules

Primary Citation

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis.

Matzov, D, Taoka, M, Nobe, Y, Yamauchi, Y, Halfon, Y, Asis, N, Zimermann, E, Rozenberg, H, Bashan, A, Bhushan, S, Isobe, T, Gray, M.W, Yonath, A, Shalev-Benami, M.Show

Nucleic Acids Res. 48 11750 11761 (2020)

PMID: 33091122 DOI: 10.1093/nar/gkaa893

Abstact

Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.

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Chemical

Disease

Primary Citation of related structures