9XJA image
Deposition Date 2025-11-04
Release Date 2026-11-11
Last Version Date 2026-11-11
Entry Detail
PDB ID:
9XJA
Keywords:
RIBOSOME
Title:
In situ portimine A-bound human pre-60S ribosome from intact HEK293T cells
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.51 Å
Aggregation State:
CELL
Reconstruction Method:
SINGLE PARTICLE
9XJA validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initia
Gene (Uniprot):EIF6
Chain IDs:UA (auth: 6)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P56537
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:D (auth: L5)
Chain Length:5069
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:E (auth: L7)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: L8)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL8
Chain IDs:A (auth: LA)
Chain Length:252
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62917
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL3
Chain IDs:B (auth: LB)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39023
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL4
Chain IDs:F (auth: LC)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P36578
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL5
Chain IDs:R (auth: LD)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46777
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL6
Chain IDs:I (auth: LE)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02878
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL7
Chain IDs:FA (auth: LF)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18124
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL7A
Chain IDs:J (auth: LG)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62424
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:H (auth: LH)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32969
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL10
Chain IDs:Q (auth: LI)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P27635
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL11
Chain IDs:G (auth: LJ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62913
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL13
Chain IDs:L (auth: LL)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P26373
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL14
Chain IDs:N (auth: LM)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P50914
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL15
Chain IDs:P (auth: LN)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61313
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL13A
Chain IDs:K (auth: LO)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P40429
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL17
Chain IDs:W (auth: LP)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18621
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL18
Chain IDs:S (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q07020
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL19
Chain IDs:T (auth: LR)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P84098
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL18A
Chain IDs:U (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02543
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL21
Chain IDs:V (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46778
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL22
Chain IDs:X (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35268
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL23
Chain IDs:M (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62829
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL24
Chain IDs:AA (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83731
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL23A
Chain IDs:Y (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62750
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL26
Chain IDs:Z (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61254
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL27
Chain IDs:BA (auth: LZ)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61353
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL27A
Chain IDs:O (auth: La)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46776
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL29
Chain IDs:EA (auth: Lb)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P47914
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL30
Chain IDs:GA (auth: Lc)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62888
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL31
Chain IDs:HA (auth: Ld)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62899
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL32
Chain IDs:IA (auth: Le)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62910
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL35A
Chain IDs:JA (auth: Lf)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18077
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL34
Chain IDs:KA (auth: Lg)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49207
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL35
Chain IDs:DA (auth: Lh)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42766
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL36
Chain IDs:LA (auth: Li)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3U8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL37
Chain IDs:MA (auth: Lj)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61927
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL38
Chain IDs:NA (auth: Lk)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63173
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL39
Chain IDs:OA (auth: Ll)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62891
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein e
Gene (Uniprot):UBA52
Chain IDs:PA (auth: Lm)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62987
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPL41
Chain IDs:QA (auth: Ln)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62945
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL36A
Chain IDs:RA (auth: Lo)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83881
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL37A
Chain IDs:SA (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61513
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL28
Chain IDs:CA (auth: Lr)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46779
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proliferation-associated prot
Gene (Uniprot):PA2G4
Chain IDs:TA (auth: z)
Chain Length:394
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UQ80
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
HIC B HIS modified residue
M3L PA LYS modified residue
MLZ EA, RA LYS modified residue
V5N A, O HIS modified residue
Ligand Molecules
A1E6S
ADP
K
PUT
SPD
SPM
ZN
Primary Citation
In situ portimine A-bound human pre-60S ribosome from intact HEK293T cells
To Be Published ? ? ? (?)
Primary Citation of related structures
9XJA
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