ISDA: 7QIZ

Deposition Date 2021-12-16

Release Date 2022-08-03

Last Version Date 2024-04-24

Entry Detail

PDB ID:

7QIZ

Keywords:

RIBOSOME

Title:

Specific features and methylation sites of a plant 80S ribosome

Biological Source:

Source Organism:

Solanum lycopersicum (Taxon ID: 4081)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.38 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:QA (auth: 2)
Chain Length:3391
Number of Molecules:1
Biological Source:Solanum lycopersicum

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:RA (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Solanum lycopersicum

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:SA (auth: 8)
Chain Length:165
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:PB (auth: AA)
Chain Length:144
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:P49215 Pfam ID:PF00833

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):101245249
Chain IDs:QB (auth: BA)
Chain Length:3
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7G7P4 Pfam ID:PF01249

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S body ribosomal protein uS12
Gene (Uniprot):101252449
Chain IDs:RB (auth: CA)
Chain Length:142
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4D3L7 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:A (auth: D)
Chain Length:260
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:P29766 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):101248302
Chain IDs:SB (auth: DA)
Chain Length:127
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GRY8 Pfam ID:PF01283

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:C (auth: E)
Chain Length:112
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:Q6SKP4 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:S5 DRBM domain-containing protein
Gene (Uniprot):101258363
Chain IDs:TB (auth: EA)
Chain Length:280
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7G7F0 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribos_L4_asso_C domain-containing protein
Gene (Uniprot):101259570
Chain IDs:B (auth: F)
Chain Length:120
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7HW81 Pfam ID:PF00573, PF14374

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):101249290
Chain IDs:UB (auth: FA)
Chain Length:249
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7HSH1 Pfam ID:PF01092

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L18_c domain-containing protein
Gene (Uniprot):101262823
Chain IDs:D (auth: G)
Chain Length:301
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7H274 Pfam ID:PF17144, PF14204

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S body ribosomal protein uS4
Gene (Uniprot):101253011
Chain IDs:VB (auth: GA)
Chain Length:197
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4ATQ2 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L6e_N domain-containing protein
Gene (Uniprot):101250600
Chain IDs:E (auth: H)
Chain Length:229
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GMA5 Pfam ID:PF03868, PF01159

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15, chloroplastic
Gene (Uniprot):101251264
Chain IDs:WB (auth: HA)
Chain Length:151
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4CYU9 Pfam ID:PF08069, PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Thaliana 60S ribosomal protein L7
Gene (Uniprot):102594660
Chain IDs:F (auth: I)
Chain Length:242
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:M1BRF8 Pfam ID:PF08079, PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S14
Gene (Uniprot):102581547
Chain IDs:XB (auth: IA)
Chain Length:150
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:Q38JI8 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L7Ae domain-containing protein
Chain IDs:G (auth: J)
Chain Length:258
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GV73 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a-1
Gene (Uniprot):LOC104246267
Chain IDs:BC (auth: JA)
Chain Length:130
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A1U7YEG5 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL6
Gene (Uniprot):101249254
Chain IDs:H (auth: K)
Chain Length:194
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7JDZ0 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):101258992
Chain IDs:YB (auth: KA)
Chain Length:133
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7I5D6 Pfam ID:PF01282

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):ACI29
Chain IDs:I (auth: L)
Chain Length:95
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:Q3SC85 Pfam ID:PF00252

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:ZB (auth: LA)
Chain Length:86
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL5
Gene (Uniprot):101259713
Chain IDs:J (auth: M)
Chain Length:69
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4CG62 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:AC (auth: MA)
Chain Length:62
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A0V0GRY5 Pfam ID:PF04758

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):101262297
Chain IDs:K (auth: N)
Chain Length:206
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7JCM5 Pfam ID:PF01294

Polymer Type:polypeptide(L)
Molecule:KH type-2 domain-containing protein
Chain IDs:UA (auth: NA)
Chain Length:239
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L14e domain-containing protein
Gene (Uniprot):101252219
Chain IDs:L (auth: O)
Chain Length:133
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7J0J5 Pfam ID:PF01929

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_S7 domain-containing protein
Gene (Uniprot):101266690
Chain IDs:VA (auth: OA)
Chain Length:211
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7IVL4 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):101259162
Chain IDs:M (auth: P)
Chain Length:204
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7HQH0 Pfam ID:PF00827

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:S10_plectin domain-containing protein
Gene (Uniprot):101253268
Chain IDs:WA (auth: PA)
Chain Length:180
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7JYM3 Pfam ID:PF03501

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pectinesterase
Chain IDs:N (auth: Q)
Chain Length:206
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7HGG4 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS19
Gene (Uniprot):101249784
Chain IDs:XA (auth: QA)
Chain Length:151
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7F5X2 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22, chloroplastic
Chain IDs:O (auth: R)
Chain Length:173
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FNQ5 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS9
Gene (Uniprot):101254200
Chain IDs:YA (auth: RA)
Chain Length:147
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GDB0 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L18e/L15P domain-containing protein
Gene (Uniprot):101267842
Chain IDs:P (auth: S)
Chain Length:187
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7I5W4 Pfam ID:PF17135

Polymer Type:polyribonucleotide
Molecule:18S
Chain IDs:TA (auth: S2)
Chain Length:1808
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19
Gene (Uniprot):101261236
Chain IDs:Q (auth: T)
Chain Length:213
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GQ29 Pfam ID:PF01280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS13
Gene (Uniprot):101266399
Chain IDs:ZA (auth: TA)
Chain Length:152
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FJL7 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):104648652
Chain IDs:R (auth: U)
Chain Length:178
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7IGB1 Pfam ID:PF01775

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS19
Gene (Uniprot):101249905
Chain IDs:AB (auth: UA)
Chain Length:143
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FTS1 Pfam ID:PF01090

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL21
Gene (Uniprot):101257121
Chain IDs:S (auth: V)
Chain Length:164
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7IJQ0 Pfam ID:PF01157

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_S10 domain-containing protein
Chain IDs:BB (auth: VA)
Chain Length:123
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7EMX2 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL22
Gene (Uniprot):101245794
Chain IDs:T (auth: W)
Chain Length:124
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7I7E8 Pfam ID:PF01776

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS28
Gene (Uniprot):101248825
Chain IDs:CB (auth: WA)
Chain Length:65
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4B4Z0 Pfam ID:PF01200

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL14
Gene (Uniprot):543752
Chain IDs:U (auth: X)
Chain Length:140
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4CUW3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS14
Gene (Uniprot):101254555
Chain IDs:DB (auth: XA)
Chain Length:56
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7ITW7 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TRASH domain-containing protein
Gene (Uniprot):101252133
Chain IDs:V (auth: Y)
Chain Length:165
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7IN69 Pfam ID:PF01246

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitogen-activated protein kinase
Chain IDs:EB (auth: YA)
Chain Length:326
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GX91 Pfam ID:PF00400

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L23eN domain-containing protein
Gene (Uniprot):101247574
Chain IDs:W (auth: Z)
Chain Length:154
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7INK3 Pfam ID:PF03939, PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):101261290
Chain IDs:FB (auth: ZA)
Chain Length:108
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7F3F2 Pfam ID:PF03297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:KOW domain-containing protein
Gene (Uniprot):101261182
Chain IDs:X (auth: a)
Chain Length:146
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FBC6 Pfam ID:PF16906, PF00467

Polymer Type:polyribonucleotide
Molecule:tRNA_1
Chain IDs:GB (auth: aA)
Chain Length:144
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):101251893
Chain IDs:Y (auth: b)
Chain Length:135
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GZ83 Pfam ID:PF01777

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:HB (auth: bA)
Chain Length:3
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L18e/L15P domain-containing protein
Gene (Uniprot):101268580
Chain IDs:Z (auth: c)
Chain Length:148
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GZ10 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):101263912
Chain IDs:AA (auth: d)
Chain Length:260
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GK12 Pfam ID:PF01779

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL30
Chain IDs:BA (auth: e)
Chain Length:112
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL31
Gene (Uniprot):101265312
Chain IDs:CA (auth: f)
Chain Length:120
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7JRW8 Pfam ID:PF01198

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL32
Gene (Uniprot):101253152
Chain IDs:DA (auth: g)
Chain Length:301
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7F2B5 Pfam ID:PF01655

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL33
Chain IDs:EA (auth: h)
Chain Length:229
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FPS6 Pfam ID:PF01247

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL34
Gene (Uniprot):101266720
Chain IDs:FA (auth: i)
Chain Length:242
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GDM4 Pfam ID:PF01199

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Similar to 60S ribosomal protein L35
Gene (Uniprot):778319
Chain IDs:GA (auth: j)
Chain Length:258
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:Q53U38 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Chain IDs:HA (auth: k)
Chain Length:194
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GUG2 Pfam ID:PF01158

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):101260522
Chain IDs:IA (auth: l)
Chain Length:95
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FV98 Pfam ID:PF01907

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:JA (auth: m)
Chain Length:69
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:P46291 Pfam ID:PF01781

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL39
Gene (Uniprot):101256892
Chain IDs:KA (auth: n)
Chain Length:206
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7J415 Pfam ID:PF00832

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):101264240
Chain IDs:LA (auth: o)
Chain Length:133
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4B017 Pfam ID:PF00240, PF01020

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL42
Gene (Uniprot):101253271
Chain IDs:MA (auth: p)
Chain Length:204
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FPL2 Pfam ID:PF00935

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL43
Gene (Uniprot):101251802
Chain IDs:NA (auth: q)
Chain Length:206
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4CND1 Pfam ID:PF01780

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L28e domain-containing protein
Gene (Uniprot):101247801
Chain IDs:OA (auth: r)
Chain Length:173
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7FVJ9 Pfam ID:PF01778

Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:PA (auth: s)
Chain Length:187
Number of Molecules:1
Biological Source:Solanum lycopersicum

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Chain IDs:IB (auth: t)
Chain Length:213
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4C3A4 Pfam ID:PF05162

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):101250808
Chain IDs:JB (auth: u)
Chain Length:178
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7H1U4 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):101252719
Chain IDs:KB (auth: v)
Chain Length:164
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7I881 Pfam ID:PF01015

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):101246828
Chain IDs:LB (auth: w)
Chain Length:124
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7GQU3 Pfam ID:PF08071, PF00900, PF00467, PF16121

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):101268693
Chain IDs:MB (auth: x)
Chain Length:140
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7H0E8 Pfam ID:PF01251

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):101250510
Chain IDs:NB (auth: y)
Chain Length:165
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:A0A3Q7HJ03 Pfam ID:PF01201

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_S17_N domain-containing protein
Gene (Uniprot):101266035
Chain IDs:OB (auth: z)
Chain Length:154
Number of Molecules:1
Biological Source:Solanum lycopersicum

UniProt ID:K4C998 Pfam ID:PF16205, PF00366

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MA	QA	A	modified residue
5MC	QA	C	modified residue
A2M	QA	A	modified residue
HIC	C	HIS	modified residue
OMC	QA	C	modified residue
OMG	QA	G	modified residue
OMU	QA	U	modified residue
PSU	QA	U	modified residue
THC	OA	THR	modified residue
UR3	QA	U	modified residue

Ligand Molecules

BGC

PUT

SPD

SPM

Primary Citation

Cryo-EM structure and rRNA modification sites of a plant ribosome.

Cottilli, P, Itoh, Y, Nobe, Y, Petrov, A.S, Lison, P, Taoka, M, Amunts, A.Show

Plant Commun. 3 100342 100342 (2022)

PMID: 35643637 DOI: 10.1016/j.xplc.2022.100342

Abstact

Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.

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Protein

Chemical

Disease

Primary Citation of related structures