8PJ4 image
Deposition Date 2023-06-22
Release Date 2024-08-14
Last Version Date 2025-01-29
Entry Detail
PDB ID:
8PJ4
Keywords:
RIBOSOME
Title:
Structure of human 48S translation initiation complex after eIF5 release (48S-4)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8PJ4 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 5B
Gene (Uniprot):EIF5B
Chain IDs:A (auth: 0)
Chain Length:1220
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60841 Pfam ID:PF00009, PF11987, PF14578 EC:3.6.5.3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit B
Gene (Uniprot):EIF3B
Chain IDs:B (auth: 1)
Chain Length:814
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55884 Pfam ID:PF00076, PF08662
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit I
Gene (Uniprot):EIF3I
Chain IDs:C (auth: 2)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13347 Pfam ID:PF00400, PF12894
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit K
Gene (Uniprot):EIF3K
Chain IDs:D (auth: 3)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UBQ5 Pfam ID:PF10075
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit F
Gene (Uniprot):EIF3F
Chain IDs:E (auth: 4)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00303 Pfam ID:PF01398, PF13012
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit L
Gene (Uniprot):EIF3L
Chain IDs:F (auth: 5)
Chain Length:564
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y262 Pfam ID:PF10255
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit M
Gene (Uniprot):EIF3M
Chain IDs:G (auth: 6)
Chain Length:374
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7L2H7 Pfam ID:PF01399, PF18005
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:H (auth: 7)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit H
Gene (Uniprot):EIF3H
Chain IDs:I (auth: 8)
Chain Length:352
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15372 Pfam ID:PF01398, PF19445
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:J (auth: 9)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62945 Pfam ID:PF05162
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:K (auth: A)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:L (auth: B)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62280 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:M (auth: C)
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:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:N (auth: D)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46781 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:O (auth: E)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62266 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS30
Gene (Uniprot):FAU
Chain IDs:P (auth: F)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62861 Pfam ID:PF00240, PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:Q (auth: G)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62081 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:R (auth: H)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42677 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:S (auth: I)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62277 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:T (auth: J)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62244 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:U (auth: K)
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 S2
Gene (Uniprot):RPS2
Chain IDs:V (auth: L)
Chain Length:293
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 S17
Gene (Uniprot):RPS17
Chain IDs:W (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08708 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:X (auth: N)
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:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:Y (auth: O)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61247 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:Z (auth: P)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62263 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:AA (auth: Q)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62854 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:BA (auth: R)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62241 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:CA (auth: S)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62753 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:DA (auth: T)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62847 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:EA (auth: V)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46782 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:FA (auth: Y)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62249 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:GA (auth: Z)
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:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:HA (auth: a)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46783 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:IA (auth: b)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62841 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:JA (auth: c)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63244 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:KA (auth: d)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39019 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:LA (auth: e)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62851 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:MA (auth: f)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62269 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:NA (auth: h)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60866 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:OA (auth: i)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62273 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):RPS27A
Chain IDs:PA (auth: k)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62979 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:QA (auth: m)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25398 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:RA (auth: n)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62857 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit G
Gene (Uniprot):EIF3G
Chain IDs:SA (auth: o)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75821 Pfam ID:PF12353, PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1A, X-chromosomal
Gene (Uniprot):EIF1AX
Chain IDs:TA (auth: q)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P47813 Pfam ID:PF01176
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 1
Gene (Uniprot):EIF2S1
Chain IDs:UA (auth: r)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P05198 Pfam ID:PF00575, PF07541 EC:3.6.5.3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 3
Gene (Uniprot):EIF2S3
Chain IDs:VA (auth: t)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P41091 Pfam ID:PF00009, PF03144, PF09173 EC:3.6.5.3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit A
Gene (Uniprot):EIF3A
Chain IDs:WA (auth: u)
Chain Length:1382
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14152 Pfam ID:PF22591, PF01399
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit E
Gene (Uniprot):EIF3E
Chain IDs:XA (auth: v)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60228 Pfam ID:PF09440, PF01399, PF21357
Polymer Type:polyribonucleotide
Molecule:Initiator Met-tRNA-i
Chain IDs:YA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit D
Gene (Uniprot):EIF3D
Chain IDs:ZA (auth: x)
Chain Length:548
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15371 Pfam ID:PF05091
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit C
Gene (Uniprot):EIF3C
Chain IDs:AB (auth: y)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99613 Pfam ID:PF05470, PF01399
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MC K C modified residue
5MU K U modified residue
6MZ K A modified residue
A2M K A modified residue
JMH K C modified residue
MA6 K A modified residue
OMC K C modified residue
OMG K G modified residue
OMU K U modified residue
PSU K U modified residue
UR3 K U modified residue
Ligand Molecules
GTP
MG
NA
ZN
Primary Citation
Structural basis for translational control by the human 48S initiation complex.
Nat.Struct.Mol.Biol. 32 62 72 (2025)
PMID: 39289545 DOI: 10.1038/s41594-024-01378-4

Abstact

The selection of an open reading frame (ORF) for translation of eukaryotic mRNA relies on remodeling of the scanning 48S initiation complex into an elongation-ready 80S ribosome. Using cryo-electron microscopy, we visualize the key commitment steps orchestrating 48S remodeling in humans. The mRNA Kozak sequence facilitates mRNA scanning in the 48S open state and stabilizes the 48S closed state by organizing the contacts of eukaryotic initiation factors (eIFs) and ribosomal proteins and by reconfiguring mRNA structure. GTPase-triggered large-scale fluctuations of 48S-bound eIF2 facilitate eIF5B recruitment, transfer of initiator tRNA from eIF2 to eIF5B and the release of eIF5 and eIF2. The 48S-bound multisubunit eIF3 complex controls ribosomal subunit joining by coupling eIF exchange to gradual displacement of the eIF3c N-terminal domain from the intersubunit interface. These findings reveal the structural mechanism of ORF selection in human cells and explain how eIF3 could function in the context of the 80S ribosome.

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Protein

Chemical

Disease

Primary Citation of related structures
8PJ4