6YAN image
Deposition Date 2020-03-12
Release Date 2020-04-08
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6YAN
Keywords:
TRANSLATION
Title:
Mammalian 48S late-stage translation initiation complex with histone 4 mRNA
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Oryctolagus cuniculus (Taxon ID: 9986)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.48 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6YAN validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:initiator methionylated tRNA
Chain IDs:MA (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:GA (auth: 2)
Chain Length:1863
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:histone 4 (H4) mRNA
Chain IDs:HA (auth: 3)
Chain Length:36
Number of Molecules:1
Biological Source:Mus musculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 1
Gene (Uniprot):EIF2S1
Chain IDs:IA (auth: A)
Chain Length:126
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T2G4 Pfam ID:PF00575, PF07541
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eukaryotic translation initiation factor 2 subunit gamma
Chain IDs:JA (auth: B)
Chain Length:422
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:A0A6P3CWF8 Pfam ID:PF00009, PF03144, PF09173
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:B (auth: C)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TLT8 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS1
Gene (Uniprot):RPS3A
Chain IDs:C (auth: D)
Chain Length:215
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TN72 Pfam ID:PF01015
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS5
Chain IDs:D (auth: E)
Chain Length:226
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:E (auth: F)
Chain Length:227
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TNM3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):RPS4X
Chain IDs:F (auth: G)
Chain Length:313
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TK17 Pfam ID:PF08071, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TFM5 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:H (auth: I)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:A0A5K1UJS7 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS7
Gene (Uniprot):RPS7
Chain IDs:I (auth: J)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SVB0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:J (auth: K)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TJW1 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S9 (Predicted)
Gene (Uniprot):RPS9
Chain IDs:K (auth: L)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:B7NZS8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS10
Chain IDs:L (auth: M)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TPV3 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:M (auth: N)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TRM4 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:N (auth: O)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SFR8 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS15
Gene (Uniprot):RPS13
Chain IDs:O (auth: P)
Chain Length:150
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SP51 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS11
Gene (Uniprot):RPS14
Chain IDs:P (auth: Q)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T1F0 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:LA (auth: R)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1U0Q2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS9
Gene (Uniprot):RPS16
Chain IDs:Q (auth: S)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SGX4 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS17
Gene (Uniprot):RPS17
Chain IDs:R (auth: T)
Chain Length:126
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TU13 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS13
Gene (Uniprot):RPS18
Chain IDs:KA (auth: U)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TPG3 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS19
Gene (Uniprot):RPS19
Chain IDs:S (auth: V)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TN62 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal_S10 domain-containing protein
Chain IDs:T (auth: W)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SIZ2 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:U (auth: X)
Chain Length:82
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TM82 Pfam ID:PF01249
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:V (auth: Y)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TG89 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS12
Gene (Uniprot):RPS23
Chain IDs:W (auth: Z)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SZ47 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:X (auth: a)
Chain Length:126
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TS40 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS26
Gene (Uniprot):RPS26
Chain IDs:Y (auth: b)
Chain Length:422
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TFE8 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:Z (auth: c)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TZ76 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS28
Gene (Uniprot):RPS28
Chain IDs:AA (auth: d)
Chain Length:215
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TIB4 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS14
Gene (Uniprot):RPS29
Chain IDs:BA (auth: e)
Chain Length:226
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1U7M4 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS31
Gene (Uniprot):RPS27A
Chain IDs:CA (auth: f)
Chain Length:227
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SK22 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein RACK1
Gene (Uniprot):RACK1
Chain IDs:DA (auth: g)
Chain Length:313
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SJB4 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS25
Gene (Uniprot):RPS25
Chain IDs:EA (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TDB3 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS30
Gene (Uniprot):FAU
Chain IDs:FA (auth: i)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T8A2 Pfam ID:PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60s ribosomal protein l41
Gene (Uniprot):RPL41
Chain IDs:A (auth: l)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:A0A087WNH4 Pfam ID:PF05162
Ligand Molecules
NA
Primary Citation
Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Cell Rep 31 107497 107497 (2020)
PMID: 32268096 DOI: 10.1016/j.celrep.2020.03.061

Abstact

In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.

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Protein

Chemical

Disease

Primary Citation of related structures
6YAL
6YAM