ISDA: 9SPF

Deposition Date 2025-09-17

Release Date 2026-01-21

Last Version Date 2026-01-21

Entry Detail

PDB ID:

9SPF

Keywords:

RIBOSOME

Title:

CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:A-site-tRNA-Ile-AAT-9-1
Chain IDs:A (auth: At)
Chain Length:77
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:E site tRNA
Chain IDs:B (auth: Et)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:C (auth: L5)
Chain Length:5069
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D (auth: L7)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:E (auth: L8)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):RPL8
Chain IDs:BC (auth: LA)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62917 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):RPL3
Chain IDs:F (auth: LB)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39023 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:G (auth: LC)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36578 Pfam ID:PF00573, PF14374

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:H (auth: LD)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46777 Pfam ID:PF17144, PF14204

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6
Gene (Uniprot):RPL6
Chain IDs:I (auth: LE)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q02878 Pfam ID:PF03868, PF01159

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):RPL7
Chain IDs:J (auth: LF)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18124 Pfam ID:PF08079, PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:K (auth: LG)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62424 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:L (auth: LH)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32969 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:M (auth: LI)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P27635 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:N (auth: LJ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62913 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13
Gene (Uniprot):RPL13
Chain IDs:O (auth: LL)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P26373 Pfam ID:PF01294

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:P (auth: LM)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50914 Pfam ID:PF01929

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:Q (auth: LN)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61313 Pfam ID:PF00827

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:R (auth: LO)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P40429 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:S (auth: LP)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18621 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:T (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q07020 Pfam ID:PF17135

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:U (auth: LR)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P84098 Pfam ID:PF01280, PF25476

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:V (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q02543 Pfam ID:PF01775

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:W (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46778 Pfam ID:PF01157

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:X (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35268 Pfam ID:PF01776

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:Y (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62829 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:Z (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P83731 Pfam ID:PF01246

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:AA (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62750 Pfam ID:PF03939, PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:BA (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61254 Pfam ID:PF16906, PF00467

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:CA (auth: LZ)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61353 Pfam ID:PF00467, PF01777

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):RPL27A
Chain IDs:DA (auth: La)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46776 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL29
Gene (Uniprot):RPL29
Chain IDs:EA (auth: Lb)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P47914 Pfam ID:PF01779

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:FA (auth: Lc)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62888 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:GA (auth: Ld)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62899 Pfam ID:PF01198

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: Le)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62910 Pfam ID:PF01655

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:IA (auth: Lf)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18077 Pfam ID:PF01247

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:JA (auth: Lg)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49207 Pfam ID:PF01199

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:KA (auth: Lh)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42766 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:LA (auth: Li)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3U8 Pfam ID:PF01158

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37
Gene (Uniprot):RPL37
Chain IDs:EC (auth: Lj)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61927 Pfam ID:PF01907

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:MA (auth: Lk)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63173 Pfam ID:PF01781

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:NA (auth: Ll)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62891 Pfam ID:PF00832

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein eL40 fusion protein
Gene (Uniprot):UBA52
Chain IDs:OA (auth: Lm)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62987 Pfam ID:PF00240, PF01020

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:PA (auth: Ln)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62945 Pfam ID:PF05162

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL42
Gene (Uniprot):RPL36A
Chain IDs:QA (auth: Lo)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P83881 Pfam ID:PF00935

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:RA (auth: Lp)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61513 Pfam ID:PF01780

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:SA (auth: Lr)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46779 Pfam ID:PF01778

Polymer Type:polyribonucleotide
Molecule:synthetic mRNA
Chain IDs:TA (auth: Mr)
Chain Length:7
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:P-site tRNA-Arg-ACG
Chain IDs:UA (auth: Pt)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:VA (auth: S2)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):RPSA
Chain IDs:CC (auth: SA)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08865 Pfam ID:PF00318, PF16122

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:WA (auth: SB)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61247 Pfam ID:PF01015

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:XA (auth: SC)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P15880 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:YA (auth: SD)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P23396 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:ZA (auth: SE)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62701 Pfam ID:PF08071, PF00900, PF00467, PF16121

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:AB (auth: SF)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46782 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:BB (auth: SG)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62753 Pfam ID:PF01092

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:CB (auth: SH)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62081 Pfam ID:PF01251

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:DB (auth: SI)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62241 Pfam ID:PF01201

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:EB (auth: SJ)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46781 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:FB (auth: SK)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46783 Pfam ID:PF03501

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:GB (auth: SL)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62280 Pfam ID:PF16205, PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:HB (auth: SM)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P25398 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:IB (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62277 Pfam ID:PF08069, PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:JB (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62263 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:KB (auth: SP)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62841 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:LB (auth: SQ)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62249 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:MB (auth: SR)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08708 Pfam ID:PF00833

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:NB (auth: SS)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62269 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:OB (auth: ST)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39019 Pfam ID:PF01090

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:PB (auth: SU)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P60866 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:QB (auth: SV)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63220 Pfam ID:PF01249

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:RB (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62244 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:DC (auth: SX)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:A0A4W2DI10 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:SB (auth: SY)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62847 Pfam ID:PF01282

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:TB (auth: SZ)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62851 Pfam ID:PF03297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:UB (auth: Sa)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62854 Pfam ID:PF01283

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:VB (auth: Sb)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42677 Pfam ID:PF01667

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:WB (auth: Sc)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62857 Pfam ID:PF01200

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:XB (auth: Sd)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62273 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Gene (Uniprot):FAU
Chain IDs:YB (auth: Se)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62861 Pfam ID:PF00240, PF04758

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):RPS27A
Chain IDs:ZB (auth: Sf)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62979 Pfam ID:PF00240, PF01599

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:AC (auth: Sg)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63244 Pfam ID:PF00400

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
HIC	F	HIS	modified residue
HY3	DC	PRO	modified residue
M3L	OA	LYS	modified residue
MLZ	EA	LYS	modified residue
V5N	DA	HIS	modified residue

Ligand Molecules

HYG

PUT

SPD

Primary Citation

N 1 -Methylpseudouridine directly modulates translation dynamics.

Rozman, B, Broennimann, K, Rajan, K.S, Nachshon, A, Saha, C, Arazi, T, Mohan, V, Geiger, T, Wollner, C.J, Richner, J.M, Westhof, E, Yonath, A, Bashan, A, Stern-Ginossar, N.Show

Nature ? ? ? (2026)

PMID: 41535458 DOI: 10.1038/s41586-025-09945-5

Abstact

The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology1. A critical feature of this approach is the incorporation of the modified nucleoside N1-methylpseudouridine (m1Ψ), which enhances antigen expression while reducing immunogenicity2-5. However, a comprehensive understanding of how m1Ψ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that m1Ψ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that m1Ψ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that m1Ψ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the m1Ψ-dependent enhancement of protein output is modulated by codon composition, and that m1Ψ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that m1Ψ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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