3J6B image
Deposition Date 2014-01-22
Release Date 2014-04-09
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3J6B
Keywords:
RIBOSOME
Title:
Structure of the yeast mitochondrial large ribosomal subunit
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
3J6B validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein RTC6, m
Gene (Uniprot):RTC6
Chain IDs:AA (auth: 0)
Chain Length:93
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O14464 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L35, mi
Gene (Uniprot):MRPL35
Chain IDs:BA (auth: 1)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06678 Pfam ID:PF01161
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L28, mi
Gene (Uniprot):MRPL28
Chain IDs:CA (auth: 2)
Chain Length:147
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36527 Pfam ID:PF09812
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L27, mi
Gene (Uniprot):MRPL27
Chain IDs:DA (auth: 3)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36526 Pfam ID:PF09809
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L51, mi
Gene (Uniprot):MRPL51
Chain IDs:EA (auth: 4)
Chain Length:140
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06090 Pfam ID:PF05047
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L3, mit
Gene (Uniprot):MRPL3
Chain IDs:FA (auth: 5)
Chain Length:390
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36516 Pfam ID:PF00636, PF00035, PF22892
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L17, mi
Gene (Uniprot):MRPL17
Chain IDs:GA (auth: 6)
Chain Length:281
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36528 Pfam ID:PF11788
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein IMG2, m
Gene (Uniprot):IMG2
Chain IDs:HA (auth: 7)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25642 Pfam ID:PF05046
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L13, mi
Gene (Uniprot):MRPL13
Chain IDs:IA (auth: 8)
Chain Length:264
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02204 Pfam ID:PF10501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L15, mi
Gene (Uniprot):MRPL15
Chain IDs:JA (auth: 9)
Chain Length:253
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36523 Pfam ID:PF00636
Polymer Type:polyribonucleotide
Molecule:21S ribosomal RNA
Chain IDs:A
Chain Length:3296
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein RML2, m
Gene (Uniprot):RML2
Chain IDs:B
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32611 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L9, mit
Gene (Uniprot):MRPL9
Chain IDs:C
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P31334 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein YmL6, m
Gene (Uniprot):YML6
Chain IDs:D
Chain Length:226
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P51998 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L7, mit
Gene (Uniprot):MRPL7
Chain IDs:E
Chain Length:20
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36519 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L6, mit
Gene (Uniprot):MRPL6
Chain IDs:F
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32904 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L50, mi
Gene (Uniprot):MRPL50
Chain IDs:G
Chain Length:139
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53724
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L23, mi
Gene (Uniprot):MRPL23
Chain IDs:H
Chain Length:163
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12487 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L38, mi
Gene (Uniprot):MRPL38
Chain IDs:I
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35996 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L10, mi
Gene (Uniprot):MRPL10
Chain IDs:J
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36520 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L16, mi
Gene (Uniprot):MRPL16
Chain IDs:K
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38064 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L8, mit
Gene (Uniprot):MRPL8
Chain IDs:L
Chain Length:238
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22353 Pfam ID:PF01196, PF18502
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein IMG1, m
Gene (Uniprot):IMG1
Chain IDs:M
Chain Length:169
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25626 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L49, mi
Gene (Uniprot):MRPL49
Chain IDs:N
Chain Length:161
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40858 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L22, mi
Gene (Uniprot):MRPL22
Chain IDs:O
Chain Length:309
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53881 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L41, mi
Gene (Uniprot):MRP20
Chain IDs:P
Chain Length:263
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32387 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L40, mi
Gene (Uniprot):MRPL40
Chain IDs:Q
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36534 Pfam ID:PF22682, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L2, mit
Gene (Uniprot):MRP7
Chain IDs:R
Chain Length:371
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P12687 Pfam ID:PF01016, PF18471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L24, mi
Gene (Uniprot):MRPL24
Chain IDs:S
Chain Length:258
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36525 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L4, mit
Gene (Uniprot):MRPL4
Chain IDs:T
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36517 Pfam ID:PF06984
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L33, mi
Gene (Uniprot):MRPL33
Chain IDs:U
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20084 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L36, mi
Gene (Uniprot):MRPL36
Chain IDs:V
Chain Length:177
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36531 Pfam ID:PF21492
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L32, mi
Gene (Uniprot):MRPL32
Chain IDs:W
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25348 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L39, mi
Gene (Uniprot):MRPL39
Chain IDs:X
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36533
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L34, mi
Gene (Uniprot):YD9727.10
Chain IDs:Y
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04598 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mitochondrial ribosomal prote
Gene (Uniprot):MRP35
Chain IDs:Z
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53921 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L20, mi
Gene (Uniprot):MRPL20
Chain IDs:KA (auth: a)
Chain Length:3296
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22354 Pfam ID:PF12824
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L25, mi
Gene (Uniprot):MRPL25
Chain IDs:LA (auth: b)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P23369 Pfam ID:PF18126
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L31, mi
Gene (Uniprot):MRPL31
Chain IDs:MA (auth: c)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14063 Pfam ID:PF09784
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial homologous reco
Gene (Uniprot):MHR1
Chain IDs:NA (auth: d)
Chain Length:226
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06630 Pfam ID:PF12829
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:OA (auth: e)
Chain Length:20
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
MG
NA
ZN
Primary Citation
Structure of the yeast mitochondrial large ribosomal subunit.
Science 343 1485 1489 (2014)
PMID: 24675956 DOI: 10.1126/science.1249410

Abstact

Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.

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Disease

Primary Citation of related structures
3J6B
1VW3
1VW4
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