9HYM image
Deposition Date 2025-01-10
Release Date 2026-01-21
Last Version Date 2026-01-21
Entry Detail
PDB ID:
9HYM
Keywords:
RIBOSOME
Title:
Structure of WT E.coli ribosome with complexed filament nascent chain at length 34, with mRNA, P-site and A-site tRNAs, and mRNA
Biological Source:
Source Organism(s):
Dictyostelium discoideum (Taxon ID: 44689)
Escherichia coli (Taxon ID: 562)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9HYM validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:A (auth: 0)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:B (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:C (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:D (auth: 3)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:E (auth: 4)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:F (auth: 6)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:G (auth: 7)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ_1
Chain IDs:H (auth: 8)
Chain Length:50
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A2X1PTA3
Polymer Type:polyribonucleotide
Molecule:Acetyl Pro-tRNA
Chain IDs:EA (auth: A)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:FA (auth: X)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:I (auth: a)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:HA (auth: b)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:J (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:K (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:L (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:M (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:N (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:O (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:P (auth: j)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:Q (auth: k)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:R (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:S (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:T (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:U (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:V (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:W (auth: q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:X (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:Y (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:Z (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:AA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Polymer Type:polyribonucleotide
Molecule:Peptidyl Pro-tRNA
Chain IDs:DA (auth: v)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:BA (auth: w)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:CA (auth: y)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Gelation factor
Gene (Uniprot):abpC
Chain IDs:GA (auth: z)
Chain Length:148
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:P13466 Pfam ID:PF00630
Ligand Molecules
NA
Primary Citation
The ribosome directs nascent chains through two folding-dependent pathways
To Be Published ? ? ? (?)
Primary Citation of related structures
9HYM
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