3J6B

Structure of the yeast mitochondrial large ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the yeast mitochondrial large ribosomal subunit.

Amunts, A.Brown, A.Bai, X.C.Llacer, J.L.Hussain, T.Emsley, P.Long, F.Murshudov, G.Scheres, S.H.Ramakrishnan, V.

(2014) Science 343: 1485-1489

  • DOI: 10.1126/science.1249410
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein RML2, mitochondrial
B
393Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RML2
Find proteins for P32611 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32611
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L9, mitochondrial
C
269Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL9
Find proteins for P31334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL9
Go to UniProtKB:  P31334
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein YmL6, mitochondrial
D
286Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YML6
Find proteins for P51998 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P51998
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L7, mitochondrial
E
292Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL7
Find proteins for P36519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36519
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L6, mitochondrial
F
214Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL6
Find proteins for P32904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32904
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L50, mitochondrial
G
139Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL50
Find proteins for P53724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL50
Go to UniProtKB:  P53724
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L23, mitochondrial
H
163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL23
Find proteins for Q12487 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL23
Go to UniProtKB:  Q12487
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L38, mitochondrial
I
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL38 (MRPL34)
Find proteins for P35996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL38
Go to UniProtKB:  P35996
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L10, mitochondrial
J
322Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL10 (MRPL18)
Find proteins for P36520 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL10
Go to UniProtKB:  P36520
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L16, mitochondrial
K
232Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL16 (RML16)
Find proteins for P38064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL16
Go to UniProtKB:  P38064
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L8, mitochondrial
L
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL8
Find proteins for P22353 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22353
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein IMG1, mitochondrial
M
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IMG1 (PETCR46)
Find proteins for P25626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25626
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L49, mitochondrial
N
161Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL49
Find proteins for P40858 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL49
Go to UniProtKB:  P40858
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L22, mitochondrial
O
309Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL22
Find proteins for P53881 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53881
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L41, mitochondrial
P
263Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRP20 (MRPL41)
Find proteins for P32387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32387
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L40, mitochondrial
Q
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL40
Find proteins for P36534 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL40
Go to UniProtKB:  P36534
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L2, mitochondrial
R
371Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRP7 (MRPL2)
Find proteins for P12687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P12687
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L24, mitochondrial
S
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL24 (MRPL14)
Find proteins for P36525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P36525
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L4, mitochondrial
T
319Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL4
Find proteins for P36517 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL4
Go to UniProtKB:  P36517
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L33, mitochondrial
U
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL33
Find proteins for P20084 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL33
Go to UniProtKB:  P20084
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L36, mitochondrial
V
177Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL36
Find proteins for P36531 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL36
Go to UniProtKB:  P36531
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L32, mitochondrial
W
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL32
Find proteins for P25348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25348
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L39, mitochondrial
X
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL39
Find proteins for P36533 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL39
Go to UniProtKB:  P36533
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L34, mitochondrial
Y
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Find proteins for Q04598 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04598
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein YNL122C
Z
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Find proteins for P53921 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53921
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein RTC6, mitochondrial
0
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RTC6 (TAE4)
Find proteins for O14464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O14464
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L35, mitochondrial
1
367Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL35
Find proteins for Q06678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL35
Go to UniProtKB:  Q06678
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L28, mitochondrial
2
147Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL28
Find proteins for P36527 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL28
Go to UniProtKB:  P36527
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L27, mitochondrial
3
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL27
Find proteins for P36526 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL27
Go to UniProtKB:  P36526
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L51, mitochondrial
4
140Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL51
Find proteins for Q06090 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL51
Go to UniProtKB:  Q06090
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L3, mitochondrial
5
390Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL3
Find proteins for P36516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL3
Go to UniProtKB:  P36516
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L17, mitochondrial
6
281Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL17 (MRPL30)
Find proteins for P36528 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL17
Go to UniProtKB:  P36528
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein IMG2, mitochondrial
7
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IMG2
Find proteins for P25642 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25642
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L13, mitochondrial
8
264Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL13
Find proteins for Q02204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL13
Go to UniProtKB:  Q02204
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L15, mitochondrial
9
253Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL15
Find proteins for P36523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL15
Go to UniProtKB:  P36523
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L20, mitochondrial
a
195Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL20
Find proteins for P22354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRPL20
Go to UniProtKB:  P22354
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L25, mitochondrial
b
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL25 (YMR26)
Find proteins for P23369 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23369
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
54S ribosomal protein L31, mitochondrial
c
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRPL31
Find proteins for P14063 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14063
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial homologous recombination protein 1
d
226Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MHR1 (XTC1)
Find proteins for Q06630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06630
Entity ID: 1
MoleculeChainsLengthOrganism
21S ribosomal RNAA3296Saccharomyces cerevisiae
Entity ID: 41
MoleculeChainsLengthOrganism
E-site tRNAe20Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
0, W
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Other
  • Version 1.2: 2014-12-10
    Type: Other
  • Version 1.3: 2014-12-17
    Type: Other
  • Version 1.4: 2018-07-18
    Type: Data collection