ISDA

Deposition Date 2023-02-14

Release Date 2023-04-19

Last Version Date 2023-11-15

Entry Detail

PDB ID:

8G60

Keywords:

RIBOSOME

Title:

mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.54 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:FC (auth: At)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eEF1A
Gene (Uniprot):EEF1A1
Chain IDs:HC (auth: EF)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P68104 Pfam ID:PF00009, PF03144, PF22594

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:B (auth: L8)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:uL2
Chain IDs:MA (auth: LA)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

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

UniProt ID:P39023 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL4
Gene (Uniprot):RPL4
Chain IDs:OA (auth: LC)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36578 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL18
Gene (Uniprot):RPL5
Chain IDs:CB (auth: LD)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46777 Pfam ID:PF17144, PF14204

Protein Blast

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

UniProt ID:Q02878 Pfam ID:PF03868, PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):RPL7
Chain IDs:QB (auth: LF)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18124 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL8
Gene (Uniprot):RPL7A
Chain IDs:SA (auth: LG)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62424 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL6
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:QA (auth: LH)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32969 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL16
Gene (Uniprot):RPL10
Chain IDs:BB (auth: LI)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P27635 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL5
Gene (Uniprot):RPL11
Chain IDs:PA (auth: LJ)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62913 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL11
Gene (Uniprot):RPL12
Chain IDs:UA (auth: LK)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P30050 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL13
Gene (Uniprot):RPL13
Chain IDs:WA (auth: LL)
Chain Length:270
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P26373 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL14
Gene (Uniprot):RPL14
Chain IDs:YA (auth: LM)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50914 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL15
Gene (Uniprot):RPL15
Chain IDs:AB (auth: LN)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61313 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL13
Gene (Uniprot):RPL13A
Chain IDs:VA (auth: LO)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P40429 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL22
Gene (Uniprot):RPL17
Chain IDs:HB (auth: LP)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18621 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL18
Gene (Uniprot):RPL18
Chain IDs:DB (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q07020 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL19
Gene (Uniprot):RPL19
Chain IDs:EB (auth: LR)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P84098 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL20
Gene (Uniprot):RPL18A
Chain IDs:FB (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q02543 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL21
Gene (Uniprot):RPL21
Chain IDs:GB (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46778 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL22
Gene (Uniprot):RPL22
Chain IDs:IB (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35268 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL14
Gene (Uniprot):RPL23
Chain IDs:XA (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62829 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL24
Gene (Uniprot):RPL24
Chain IDs:LB (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P83731 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23
Gene (Uniprot):RPL23A
Chain IDs:JB (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62750 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL24
Gene (Uniprot):RPL26
Chain IDs:KB (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61254 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL27
Gene (Uniprot):RPL27
Chain IDs:MB (auth: LZ)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61353 Pfam ID:PF00467, PF01777

Protein Blast

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

UniProt ID:P46776 Pfam ID:PF00828

Protein Blast

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

UniProt ID:P47914 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL30
Gene (Uniprot):RPL30
Chain IDs:RB (auth: Lc)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62888 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):RPL31
Chain IDs:SB (auth: Ld)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62899 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL32
Gene (Uniprot):RPL32
Chain IDs:TB (auth: Le)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62910 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL33
Gene (Uniprot):RPL35A
Chain IDs:UB (auth: Lf)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18077 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL34
Gene (Uniprot):RPL34
Chain IDs:VB (auth: Lg)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49207 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):RPL35
Chain IDs:OB (auth: Lh)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42766 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL36
Gene (Uniprot):RPL36
Chain IDs:WB (auth: Li)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3U8 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL37
Gene (Uniprot):RPL37
Chain IDs:XB (auth: Lj)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61927 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL38
Gene (Uniprot):RPL38
Chain IDs:YB (auth: Lk)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63173 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):RPL39
Chain IDs:ZB (auth: Ll)
Chain Length:270
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62891 Pfam ID:PF00832

Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:AC (auth: Lm)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL41
Gene (Uniprot):RPL41
Chain IDs:BC (auth: Ln)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62945 Pfam ID:PF05162

Protein Blast

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

UniProt ID:J3KQN4 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL43
Gene (Uniprot):RPL37A
Chain IDs:DC (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61513 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL10
Gene (Uniprot):RPLP0
Chain IDs:TA (auth: Lq)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P05388 Pfam ID:PF00466, PF17777, PF00428

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL28
Gene (Uniprot):RPL28
Chain IDs:NB (auth: Lr)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46779 Pfam ID:PF01778

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL1
Gene (Uniprot):RPL10A
Chain IDs:LA (auth: Lz)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62906 Pfam ID:PF00687

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:GC (auth: Pt)
Chain Length:77
Number of Molecules:1
Biological Source:Homo sapiens

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

Protein Blast

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

UniProt ID:P08865 Pfam ID:PF00318, PF16122

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS1
Gene (Uniprot):RPS3A
Chain IDs:E (auth: SB)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61247 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS5
Gene (Uniprot):RPS2
Chain IDs:J (auth: SC)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P15880 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS3
Gene (Uniprot):RPS3
Chain IDs:G (auth: SD)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P23396 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS4
Gene (Uniprot):RPS4X
Chain IDs:I (auth: SE)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS7
Gene (Uniprot):RPS5
Chain IDs:L (auth: SF)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46782 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS6
Gene (Uniprot):RPS6
Chain IDs:K (auth: SG)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62753 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS7
Gene (Uniprot):RPS7
Chain IDs:M (auth: SH)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62081 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS8
Gene (Uniprot):RPS8
Chain IDs:O (auth: SI)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62241 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS4
Gene (Uniprot):RPS9
Chain IDs:H (auth: SJ)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46781 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS10
Gene (Uniprot):RPS10
Chain IDs:R (auth: SK)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46783 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS17
Gene (Uniprot):RPS11
Chain IDs:Y (auth: SL)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62280 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS12
Gene (Uniprot):RPS12
Chain IDs:U (auth: SM)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P25398 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS15
Gene (Uniprot):RPS13
Chain IDs:X (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62277 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS11
Gene (Uniprot):RPS14
Chain IDs:S (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62263 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS19
Gene (Uniprot):RPS15
Chain IDs:AA (auth: SP)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62841 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS9
Gene (Uniprot):RPS16
Chain IDs:P (auth: SQ)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62249 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS17
Gene (Uniprot):RPS17
Chain IDs:Z (auth: SR)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08708 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS13
Gene (Uniprot):RPS18
Chain IDs:V (auth: SS)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62269 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS19
Gene (Uniprot):RPS19
Chain IDs:BA (auth: ST)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39019 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS10
Gene (Uniprot):RPS20
Chain IDs:Q (auth: SU)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P60866 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS21
Gene (Uniprot):RPS21
Chain IDs:CA (auth: SV)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63220 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS8
Gene (Uniprot):RPS15A
Chain IDs:N (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62244 Pfam ID:PF00410

Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:T (auth: SX)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS24
Gene (Uniprot):RPS24
Chain IDs:DA (auth: SY)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62847 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS25
Gene (Uniprot):RPS25
Chain IDs:EA (auth: SZ)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62851 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS26
Gene (Uniprot):RPS26
Chain IDs:FA (auth: Sa)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62854 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS27
Gene (Uniprot):RPS27
Chain IDs:GA (auth: Sb)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42677 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS28
Gene (Uniprot):RPS28
Chain IDs:HA (auth: Sc)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62857 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):RPS29
Chain IDs:W (auth: Sd)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62273 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS30
Gene (Uniprot):FAU
Chain IDs:IA (auth: Se)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62861 Pfam ID:PF00240, PF04758

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS31
Gene (Uniprot):RPS27A
Chain IDs:JA (auth: Sf)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62979 Pfam ID:PF00240, PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RACK1
Gene (Uniprot):RACK1
Chain IDs:KA (auth: Sg)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63244 Pfam ID:PF00400

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:EC (auth: mR)
Chain Length:60
Number of Molecules:1
Biological Source:Homo sapiens

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
AME	CA	MET	modified residue
HIC	NA	HIS	modified residue
M3L	HC	LYS	modified residue
MLY	HC	LYS	modified residue
MLZ	PB	LYS	modified residue
OMG	B	G	modified residue
OMU	B	U	modified residue
PSU	B	U	modified residue
SAC	F	SER	modified residue
V5N	ZA	HIS	modified residue

Ligand Molecules

3H3

ANM

GSP

MET

PHE

PUT

SPD

ZIY

Primary Citation

mRNA decoding in human is kinetically and structurally distinct from bacteria.

Holm, M, Natchiar, S.K, Rundlet, E.J, Myasnikov, A.G, Watson, Z.L, Altman, R.B, Wang, H.Y, Taunton, J, Blanchard, S.C.Show

Nature 617 200 207 (2023)

PMID: 37020024 DOI: 10.1038/s41586-023-05908-w

Abstact

In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems1. Although key features are conserved across evolution2, eukaryotes achieve higher-fidelity mRNA decoding than bacteria3. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment4-6. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.

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