ISDA

Deposition Date 2023-02-14

Release Date 2023-04-19

Last Version Date 2023-11-15

Entry Detail

PDB ID:

8G5Z

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.64 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:eIF5A1
Chain IDs:HC (auth: 5A)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor 1-alpha 1
Gene (Uniprot):EEF1A1
Chain IDs:IC (auth: EF)
Chain Length:444
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P68105 Pfam ID:PF00009, PF03144, PF22594

Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:C (auth: L5)
Chain Length:3687
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:147
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:NA (auth: LB)
Chain Length:402
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39023 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:OA (auth: LC)
Chain Length:368
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36578 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:CB (auth: LD)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46777 Pfam ID:PF17144, PF14204

Polymer Type:polypeptide(L)
Molecule:eL6
Chain IDs:RA (auth: LE)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:QB (auth: LF)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18124 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:SA (auth: LG)
Chain Length:114
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62424 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:QA (auth: LH)
Chain Length:122
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32969 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:BB (auth: LI)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P27635 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:PA (auth: LJ)
Chain Length:169
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62913 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:UA (auth: LK)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P30050 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:WA (auth: LL)
Chain Length:50
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P26373 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:YA (auth: LM)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50914 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:AB (auth: LN)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61313 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:VA (auth: LO)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P40429 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:HB (auth: LP)
Chain Length:91
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18621 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:DB (auth: LQ)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q07020 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:EB (auth: LR)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P84098 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
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:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:GB (auth: LT)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46778 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:IB (auth: LU)
Chain Length:99
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35268 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
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

Polymer Type:polypeptide(L)
Molecule:eL24
Chain IDs:LB (auth: LW)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:uL23
Chain IDs:JB (auth: LX)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:KB (auth: LY)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61254 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:MB (auth: LZ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61353 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:ZA (auth: La)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46776 Pfam ID:PF00828

Polymer Type:polypeptide(L)
Molecule:eL29
Chain IDs:PB (auth: Lb)
Chain Length:402
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:RB (auth: Lc)
Chain Length:368
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62888 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:SB (auth: Ld)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62899 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:TB (auth: Le)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62910 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:UB (auth: Lf)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18077 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:VB (auth: Lg)
Chain Length:114
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49207 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:OB (auth: Lh)
Chain Length:122
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42766 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:WB (auth: Li)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3U8 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:XB (auth: Lj)
Chain Length:169
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61927 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:YB (auth: Lk)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63173 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:ZB (auth: Ll)
Chain Length:50
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:136
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:BC (auth: Ln)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62945 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L36a
Gene (Uniprot):RPL36A
Chain IDs:CC (auth: Lo)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:J3KQN4 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:DC (auth: Lp)
Chain Length:91
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61513 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPLP0
Chain IDs:TA (auth: Lq)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P05388 Pfam ID:PF00466, PF17777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:NB (auth: Lr)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46779 Pfam ID:PF01778

Polymer Type:polypeptide(L)
Molecule:uL1
Chain IDs:LA (auth: Lz)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

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

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: S2)
Chain Length:1701
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:F (auth: SA)
Chain Length:99
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08865 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:E (auth: SB)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61247 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:J (auth: SC)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P15880 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:G (auth: SD)
Chain Length:55
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P23396 Pfam ID:PF07650, PF00189

Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:I (auth: SE)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:L (auth: SF)
Chain Length:189
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46782 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:K (auth: SG)
Chain Length:237
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62753 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:M (auth: SH)
Chain Length:189
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62081 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:O (auth: SI)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62241 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:H (auth: SJ)
Chain Length:185
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46781 Pfam ID:PF00163, PF01479

Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:R (auth: SK)
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:uS17
Chain IDs:Y (auth: SL)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:eS12
Chain IDs:U (auth: SM)
Chain Length:122
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:X (auth: SN)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62277 Pfam ID:PF08069, PF00312

Polymer Type:polypeptide(L)
Molecule:uS11
Chain IDs:S (auth: SO)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:uS19
Chain IDs:AA (auth: SP)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:uS9
Chain IDs:P (auth: SQ)
Chain Length:141
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:Z (auth: SR)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08708 Pfam ID:PF00833

Polymer Type:polypeptide(L)
Molecule:uS13
Chain IDs:V (auth: SS)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:BA (auth: ST)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39019 Pfam ID:PF01090

Polymer Type:polypeptide(L)
Molecule:uS10
Chain IDs:Q (auth: SU)
Chain Length:101
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
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:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:N (auth: SW)
Chain Length:129
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:142
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:DA (auth: SY)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62847 Pfam ID:PF01282

Polymer Type:polypeptide(L)
Molecule:eS25
Chain IDs:EA (auth: SZ)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:FA (auth: Sa)
Chain Length:99
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62854 Pfam ID:PF01283

Polymer Type:polypeptide(L)
Molecule:eS27
Chain IDs:GA (auth: Sb)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:HA (auth: Sc)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62857 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:W (auth: Sd)
Chain Length:55
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62273 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:IA (auth: Se)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62861 Pfam ID:PF04758

Polymer Type:polypeptide(L)
Molecule:eS31
Chain IDs:JA (auth: Sf)
Chain Length:189
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:KA (auth: Sg)
Chain Length:237
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:11
Number of Molecules:1
Biological Source:Homo sapiens

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	FC	U	modified residue
AME	CA	MET	modified residue
G7M	FC	G	modified residue
H2U	FC	U	modified residue
HIC	NA	HIS	modified residue
M3L	IC	LYS	modified residue
MIA	FC	A	modified residue
MLY	IC	LYS	modified residue
MLZ	CC	LYS	modified residue
OMC	GC	C	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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures