ISDA

Deposition Date 2023-06-22

Release Date 2024-08-14

Last Version Date 2024-10-02

Entry Detail

PDB ID:

8PJ1

Keywords:

RIBOSOME

Title:

Structure of human 48S translation initiation complex in open codon scanning state (48S-1)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit B
Gene (Uniprot):EIF3B
Chain IDs:A (auth: 1)
Chain Length:814
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P55884 Pfam ID:PF00076, PF08662

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit I
Gene (Uniprot):EIF3I
Chain IDs:B (auth: 2)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13347 Pfam ID:PF00400, PF12894

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit K
Gene (Uniprot):EIF3K
Chain IDs:C (auth: 3)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UBQ5 Pfam ID:PF10075

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit F
Gene (Uniprot):EIF3F
Chain IDs:D (auth: 4)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O00303 Pfam ID:PF01398, PF13012

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit L
Gene (Uniprot):EIF3L
Chain IDs:E (auth: 5)
Chain Length:564
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y262 Pfam ID:PF10255

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit M
Gene (Uniprot):EIF3M
Chain IDs:F (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:G (auth: 7)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit H
Gene (Uniprot):EIF3H
Chain IDs:H (auth: 8)
Chain Length:352
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O15372 Pfam ID:PF01398, PF19445

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:I (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:J (auth: A)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:K (auth: B)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62280 Pfam ID:PF16205, PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:L (auth: C)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:M (auth: D)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46781 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:N (auth: E)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62266 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:P62861 Pfam ID:PF04758

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:P (auth: G)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62081 Pfam ID:PF01251

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:Q (auth: H)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42677 Pfam ID:PF01667

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:R (auth: I)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62277 Pfam ID:PF08069, PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:S (auth: J)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62244 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:T (auth: K)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63220 Pfam ID:PF01249

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:U (auth: L)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P15880 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:V (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08708 Pfam ID:PF00833

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:W (auth: N)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08865 Pfam ID:PF00318, PF16122

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:X (auth: O)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61247 Pfam ID:PF01015

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:Y (auth: P)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62263 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:Z (auth: Q)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62854 Pfam ID:PF01283

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:AA (auth: R)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62241 Pfam ID:PF01201

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:BA (auth: S)
Chain Length:333
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62753 Pfam ID:PF01092

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:CA (auth: T)
Chain Length:472
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62847 Pfam ID:PF01282

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:DA (auth: V)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46782 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:EA (auth: Y)
Chain Length:913
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62249 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:FA (auth: Z)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P23396 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:GA (auth: a)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46783 Pfam ID:PF03501

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:HA (auth: b)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62841 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:IA (auth: c)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63244 Pfam ID:PF00400

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:JA (auth: d)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39019 Pfam ID:PF01090

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:KA (auth: e)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62851 Pfam ID:PF03297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:LA (auth: f)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62269 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:MA (auth: h)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P60866 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:NA (auth: i)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62273 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):RPS27A
Chain IDs:OA (auth: k)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62979 Pfam ID:PF00240, PF01599

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:PA (auth: m)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P25398 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:QA (auth: n)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62857 Pfam ID:PF01200

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit G
Gene (Uniprot):EIF3G
Chain IDs:RA (auth: o)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75821 Pfam ID:PF12353, PF00076

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1
Gene (Uniprot):EIF1
Chain IDs:SA (auth: p)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P41567 Pfam ID:PF01253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1A, X-chromosomal
Gene (Uniprot):EIF1AX
Chain IDs:TA (auth: q)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P47813 Pfam ID:PF01176

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 2
Gene (Uniprot):EIF2S2
Chain IDs:VA (auth: s)
Chain Length:333
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P20042 Pfam ID:PF01873 EC:3.6.5.3

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 3
Gene (Uniprot):EIF2S3
Chain IDs:WA (auth: t)
Chain Length:472
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P41091 Pfam ID:PF00009, PF03144, PF09173 EC:3.6.5.3

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit A
Gene (Uniprot):EIF3A
Chain IDs:XA (auth: u)
Chain Length:1382
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q14152 Pfam ID:PF22591, PF01399

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit E
Gene (Uniprot):EIF3E
Chain IDs:YA (auth: v)
Chain Length:445
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:ZA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit D
Gene (Uniprot):EIF3D
Chain IDs:AB (auth: x)
Chain Length:548
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O15371 Pfam ID:PF05091

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit C
Gene (Uniprot):EIF3C
Chain IDs:BB (auth: y)
Chain Length:913
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
5MC	J	C	modified residue
5MU	J	U	modified residue
6MZ	J	A	modified residue
A2M	J	A	modified residue
JMH	J	C	modified residue
MA6	J	A	modified residue
OMC	J	C	modified residue
OMG	J	G	modified residue
OMU	J	U	modified residue
PSU	J	U	modified residue
UR3	J	U	modified residue

Ligand Molecules

GTP

MET

Primary Citation

Structural basis for translational control by the human 48S initiation complex.

Petrychenko, V, Yi, S.H, Liedtke, D, Peng, B.Z, Rodnina, M.V, Fischer, N.Show

Nat.Struct.Mol.Biol. ? ? ? (2024)

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