7UCK image
Deposition Date 2022-03-16
Release Date 2022-06-01
Last Version Date 2024-12-25
Entry Detail
PDB ID:
7UCK
Title:
80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:B (auth: 1)
Chain Length:6
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:A (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:28s rRNA
Chain IDs:C (auth: 5)
Chain Length:3546
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:E (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:F (auth: 9)
Chain Length:1698
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:G (auth: A)
Chain Length:147
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S_SA_C domain-containing protein
Chain IDs:WA (auth: AA)
Chain Length:101
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS26
Gene (Uniprot):RPS26
Chain IDs:VB (auth: Aa)
Chain Length:101
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:H (auth: B)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:XA (auth: BB)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:WB (auth: Bb)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Chain IDs:I (auth: C)
Chain Length:360
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:YA (auth: CC)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:XB (auth: Cc)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal_L18_c domain-containing protein
Chain IDs:J (auth: D)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:ZA (auth: DD)
Chain Length:228
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:YB (auth: Dd)
Chain Length:228
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:K (auth: E)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Chain IDs:AB (auth: EE)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:ZB (auth: Ee)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:L (auth: F)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:BB (auth: FF)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Chain IDs:M (auth: G)
Chain Length:234
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:CB (auth: GG)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:AC (auth: Gg)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9
Chain IDs:N (auth: H)
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:DB (auth: HH)
Chain Length:189
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:O (auth: I)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:EB (auth: II)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:P (auth: J)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:FB (auth: JJ)
Chain Length:185
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Chain IDs:GB (auth: KK)
Chain Length:96
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:Q (auth: L)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:HB (auth: LL)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Chain IDs:R (auth: M)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:S (auth: N)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:IB (auth: NN)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Chain IDs:T (auth: O)
Chain Length:103
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Chain IDs:JB (auth: OO)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:U (auth: P)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:KB (auth: PP)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:V (auth: Q)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Chain IDs:LB (auth: QQ)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:W (auth: R)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:MB (auth: RR)
Chain Length:132
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Chain IDs:X (auth: S)
Chain Length:176
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:NB (auth: SS)
Chain Length:144
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:Y (auth: T)
Chain Length:159
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Chain IDs:OB (auth: TT)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Chain IDs:Z (auth: U)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:PB (auth: UU)
Chain Length:100
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:AA (auth: V)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS21
Gene (Uniprot):RPS21
Chain IDs:QB (auth: VV)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:BA (auth: W)
Chain Length:121
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:RB (auth: WW)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Chain IDs:CA (auth: X)
Chain Length:118
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:SB (auth: XX)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:DA (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):LOC100338405
Chain IDs:TB (auth: YY)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:EA (auth: Z)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:UB (auth: ZZ)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:FA (auth: a)
Chain Length:147
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:GA (auth: b)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:HA (auth: c)
Chain Length:360
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:IA (auth: d)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Chain IDs:JA (auth: e)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: f)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:LA (auth: g)
Chain Length:234
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:MA (auth: h)
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:NA (auth: i)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:OA (auth: j)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Chain IDs:PA (auth: k)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):LOC100343258
Chain IDs:QA (auth: l)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L40
Chain IDs:RA (auth: m)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL41
Gene (Uniprot):RPL41
Chain IDs:SA (auth: n)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36a
Gene (Uniprot):RPL36A
Chain IDs:TA (auth: o)
Chain Length:103
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:UA (auth: p)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:VA (auth: r)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ I LYS modified residue
Primary Citation
Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine.
Mol.Cell 82 2797 2814.e11 (2022)
PMID: 35679869 DOI: 10.1016/j.molcel.2022.05.016

Abstact

mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.

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Protein

Chemical

Disease

Primary Citation of related structures