9YDB image
Deposition Date 2025-09-22
Release Date 2026-09-30
Last Version Date 2026-09-30
Entry Detail
PDB ID:
9YDB
Keywords:
RIBOSOME
Title:
Eukaryotic pre-60S ribosomes from uL16 P-site loop mutants in bypass condition. Lsg1,Nmd3 and Tif6 present
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.83 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9YDB validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S RNA
Chain IDs:A
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5S RNA
Chain IDs:B
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:8S RNA
Chain IDs:C
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:E (auth: LD)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:F (auth: LE)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14126 Pfam ID:PF00297
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:G (auth: LF)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:H (auth: LG)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL6B
Chain IDs:I (auth: LH)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05739 Pfam ID:PF01159
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:J (auth: LI)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:K (auth: LJ)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:L (auth: LK)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL10
Chain IDs:M (auth: LL)
Chain Length:210
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P41805 Pfam ID:PF00252
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL11B
Chain IDs:N (auth: LM)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q3E757 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:O (auth: LN)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12690 Pfam ID:PF01294
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:P (auth: LO)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:Q (auth: LP)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05748 Pfam ID:PF00827
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:R (auth: LQ)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:S (auth: LR)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05740 Pfam ID:PF00237
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:T (auth: LS)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX49 Pfam ID:PF17135
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:U (auth: LT)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX82 Pfam ID:PF01280, PF25476
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:V (auth: LU)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX23 Pfam ID:PF01775
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:W (auth: LV)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02753 Pfam ID:PF01157
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:X (auth: LW)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05749 Pfam ID:PF01776
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:Y (auth: LX)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX41 Pfam ID:PF00238
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:Z (auth: LY)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04449 Pfam ID:PF01246
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:AA (auth: LZ)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:BA (auth: La)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:CA (auth: Lb)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H6 Pfam ID:PF01777
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:DA (auth: Lc)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P02406 Pfam ID:PF00828
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:EA (auth: Ld)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05747 Pfam ID:PF01779
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:FA (auth: Le)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:GA (auth: Lf)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H8 Pfam ID:PF01198
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: Lg)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38061 Pfam ID:PF01655
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:IA (auth: Lh)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05744 Pfam ID:PF01247
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:JA (auth: Li)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P87262 Pfam ID:PF01199
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: Lj)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX84 Pfam ID:PF00831
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:LA (auth: Lk)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05745 Pfam ID:PF01158
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:MA (auth: Ll)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49166 Pfam ID:PF01907
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:NA (auth: Lm)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49167 Pfam ID:PF01781
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:OA (auth: Ln)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04650 Pfam ID:PF00832
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal prote
Gene (Uniprot):RPL40A
Chain IDs:PA (auth: Lo)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:QA (auth: Lq)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX27 Pfam ID:PF00935
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:RA (auth: Lr)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX25 Pfam ID:PF01780
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal export protein
Gene (Uniprot):NMD3
Chain IDs:UA (auth: V)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38861 Pfam ID:PF04981, PF21193, PF21192
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large subunit GTPase 1
Gene (Uniprot):LSG1
Chain IDs:TA (auth: W)
Chain Length:640
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P53145 Pfam ID:PF01926 EC:3.6.1.-
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initia
Gene (Uniprot):TIF6
Chain IDs:SA (auth: X)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12522 Pfam ID:PF01912
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytoplasmic 60S subunit bioge
Gene (Uniprot):REH1
Chain IDs:D (auth: z)
Chain Length:432
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q06709 Pfam ID:PF12756
Ligand Molecules
3HE
Primary Citation
Cryo-EM structure of 60S ribosomal subunit with Rpl10 loop deletion produced in bypass mutatn
To Be Published ? ? ? (?)
Primary Citation of related structures
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