8XXN image
Deposition Date 2024-01-18
Release Date 2024-05-01
Last Version Date 2024-07-10
Entry Detail
PDB ID:
8XXN
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the human 43S ribosome with PDCD4
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8XXN validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit A
Gene (Uniprot):EIF3A
Chain IDs:MA (auth: 3A)
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 B
Gene (Uniprot):EIF3B
Chain IDs:NA (auth: 3B)
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 C
Gene (Uniprot):EIF3C
Chain IDs:OA (auth: 3C)
Chain Length:913
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99613 Pfam ID:PF05470, PF01399
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit E
Gene (Uniprot):EIF3E
Chain IDs:PA (auth: 3E)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60228 Pfam ID:PF09440, PF01399, PF21357
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit F
Gene (Uniprot):EIF3F
Chain IDs:QA (auth: 3F)
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 G
Gene (Uniprot):EIF3G
Chain IDs:RA (auth: 3G)
Chain Length:320
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 3 subunit H
Gene (Uniprot):EIF3H
Chain IDs:SA (auth: 3H)
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:Eukaryotic translation initiation factor 3 subunit I
Gene (Uniprot):EIF3I
Chain IDs:TA (auth: 3I)
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:UA (auth: 3K)
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 L
Gene (Uniprot):EIF3L
Chain IDs:VA (auth: 3L)
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:WA (auth: 3M)
Chain Length:374
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7L2H7 Pfam ID:PF01399, PF18005
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit D
Gene (Uniprot):EIF3D
Chain IDs:XA (auth: 3N)
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 initiation factor 4A-I
Gene (Uniprot):EIF4A1
Chain IDs:KA (auth: 4A)
Chain Length:406
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60842 Pfam ID:PF00270, PF00271
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1
Gene (Uniprot):EIF1
Chain IDs:JA (auth: C1)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P41567 Pfam ID:PF01253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Programmed cell death protein 4
Gene (Uniprot):PDCD4
Chain IDs:LA (auth: CD)
Chain Length:469
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q53EL6 Pfam ID:PF02847
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:A (auth: Ln)
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:B (auth: S2)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:C (auth: SA)
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:D (auth: SB)
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 S2
Gene (Uniprot):RPS2
Chain IDs:X (auth: SC)
Chain Length:69
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:E (auth: SD)
Chain Length:56
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 S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:F (auth: SE)
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 S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: SF)
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 S6
Gene (Uniprot):RPS6
Chain IDs:Y (auth: SG)
Chain Length:317
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:H (auth: SH)
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 S8
Gene (Uniprot):RPS8
Chain IDs:I (auth: SI)
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 S9
Gene (Uniprot):RPS9
Chain IDs:Z (auth: SJ)
Chain Length:194
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 S10
Gene (Uniprot):RPS10
Chain IDs:J (auth: SK)
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 S11
Gene (Uniprot):RPS11
Chain IDs:K (auth: SL)
Chain Length:158
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 S12
Gene (Uniprot):RPS12
Chain IDs:AA (auth: SM)
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 S13
Gene (Uniprot):RPS13
Chain IDs:BA (auth: SN)
Chain Length:151
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 S14
Gene (Uniprot):RPS14
Chain IDs:CA (auth: SO)
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 S15
Gene (Uniprot):RPS15
Chain IDs:L (auth: SP)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62841 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:M (auth: SQ)
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 S17
Gene (Uniprot):RPS17
Chain IDs:N (auth: SR)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08708 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:O (auth: SS)
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 S19
Gene (Uniprot):RPS19
Chain IDs:P (auth: ST)
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 S20
Gene (Uniprot):RPS20
Chain IDs:Q (auth: SU)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60866 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:R (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:DA (auth: SW)
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 S23
Gene (Uniprot):RPS23
Chain IDs:S (auth: SX)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62266 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:EA (auth: SY)
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 S25
Gene (Uniprot):RPS25
Chain IDs:FA (auth: SZ)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62851 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:T (auth: Sa)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62854 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:GA (auth: Sb)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42677 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:U (auth: Sc)
Chain Length:69
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:V (auth: Sd)
Chain Length:56
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:HA (auth: Se)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62861 Pfam ID:PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:IA (auth: Sf)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62979 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:W (auth: Sg)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63244 Pfam ID:PF00400
Ligand Molecules
MG
ZN
Primary Citation
Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
Cell Res. 34 522 525 (2024)
PMID: 38641729 DOI: 10.1038/s41422-024-00962-z
Primary Citation of related structures
8XXN