5MRF

Structure of the yeast mitochondrial ribosome - Class C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.97 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

The structure of the yeast mitochondrial ribosome.

Desai, N.Brown, A.Amunts, A.Ramakrishnan, V.

(2017) Science 355: 528-531

  • DOI: https://doi.org/10.1126/science.aal2415
  • Primary Citation of Related Structures:  
    5MRC, 5MRE, 5MRF

  • PubMed Abstract: 

    Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL2m393Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL3m249Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL4m252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL5m274Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL6m196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
bL9m74Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL13m160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL14m138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL15m220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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uL16m195Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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bL17m237Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL19m151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
bL21m118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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uL22m225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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uL23m207Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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uL24m296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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bL27m337Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
bL28m216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL29m225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL30m82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL31m177Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
bL32m112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
bL33m64Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
bL34m46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
bL35m62Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mAA [auth 0]38Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mL38BA [auth 1]348Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
mL40CA [auth 2]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL41DA [auth 3]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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mL43EA [auth 4]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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mL44FA [auth 5]324Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL46GA [auth 6]281Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL49HA [auth 7]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
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mL50IA [auth 8]264Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
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mL57JA [auth 9]215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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mL58KA [auth a]177Saccharomyces cerevisiaeMutation(s): 0 
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mL59LA [auth b]155Saccharomyces cerevisiaeMutation(s): 0 
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mL60MA [auth c]119Saccharomyces cerevisiaeMutation(s): 0 
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mL67NA [auth d]215Saccharomyces cerevisiaeMutation(s): 0 
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bS1mOA [auth AA]344Saccharomyces cerevisiaeMutation(s): 0 
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uS2mPA [auth BB]266Saccharomyces cerevisiaeMutation(s): 0 
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uS3mQA [auth CC]398Saccharomyces cerevisiaeMutation(s): 0 
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uS4mRA [auth DD]486Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
uS5mSA [auth EE]293Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
bS6mTA [auth FF]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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uS7mUA [auth GG]161Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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uS8mVA [auth HH]154Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mWA [auth II]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mXA [auth JJ]186Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mYA [auth KK]148Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
uS12mZA [auth LL]124Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
uS13mAB [auth MM]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mBB [auth NN]115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mCB [auth OO]253Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mDB [auth PP]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mEB [auth QQ]237Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
bS18mFB [auth RR]99Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS19mGB [auth SS]80Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mHB [auth TT]92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mS23IB [auth UU]233Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
mS26JB [auth VV]233Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
mS29KB [auth WW]401Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
mS33LB [auth XX]96Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
mS35MB [auth YY]273Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
mS37NB [auth ZZ]91Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
mS38OB [auth 11]34Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
mS41PB [auth 22]99Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
mS42QB [auth 33]255Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
mS43RB [auth 44]321Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
mS44SB [auth 55]339Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
mS45TB [auth 66]319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
mS46UB [auth 77]165Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mS47VB [auth 88]457Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.2.4
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
unknown protein sequence 1YB [auth cc]94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
unknown protein sequence 2ZB [auth dd]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
21S ribosomal RNA3,296Saccharomyces cerevisiae
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Entity ID: 75
MoleculeChains LengthOrganismImage
15S ribosomal RNAWB [auth aa]1,649Saccharomyces cerevisiae
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Entity ID: 76
MoleculeChains LengthOrganismImage
tRNAXB [auth bb]76Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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JJ [auth WW]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

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CJ [auth W],
DJ [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AK [auth aa],
AL [auth aa],
AM [auth aa],
AN [auth aa],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth R],
BK [auth aa],
BL [auth aa],
BM [auth aa],
BN [auth aa],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CK [auth aa],
CL [auth aa],
CM [auth aa],
CN [auth aa],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
DK [auth aa],
DL [auth aa],
DM [auth aa],
DN [auth aa],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth BB],
EK [auth aa],
EL [auth aa],
EM [auth aa],
EN [auth aa],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
FJ [auth LL],
FK [auth aa],
FL [auth aa],
FM [auth aa],
FN [auth aa],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth MM],
GK [auth aa],
GL [auth aa],
GM [auth aa],
GN [auth aa],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth OO],
HK [auth aa],
HL [auth aa],
HM [auth aa],
HN [auth aa],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth PP],
IK [auth aa],
IL [auth aa],
IM [auth aa],
IN [auth aa],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JK [auth aa],
JL [auth aa],
JM [auth aa],
JN [auth aa],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth WW],
KK [auth aa],
KL [auth aa],
KM [auth aa],
KN [auth aa],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth aa],
LK [auth aa],
LL [auth aa],
LM [auth aa],
LN [auth aa],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth aa],
MK [auth aa],
ML [auth aa],
MM [auth aa],
MN [auth aa],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth aa],
NK [auth aa],
NL [auth aa],
NM [auth aa],
NN [auth aa],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth aa],
OK [auth aa],
OL [auth aa],
OM [auth aa],
ON [auth aa],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth aa],
PK [auth aa],
PL [auth aa],
PM [auth aa],
PN [auth aa],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth aa],
QK [auth aa],
QL [auth aa],
QM [auth aa],
QN [auth aa],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth aa],
RK [auth aa],
RL [auth aa],
RM [auth aa],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth aa],
SK [auth aa],
SL [auth aa],
SM [auth aa],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth aa],
TK [auth aa],
TL [auth aa],
TM [auth aa],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth aa],
UK [auth aa],
UL [auth aa],
UM [auth aa],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth aa],
VK [auth aa],
VL [auth aa],
VM [auth aa],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth aa],
WK [auth aa],
WL [auth aa],
WM [auth aa],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth aa],
XK [auth aa],
XL [auth aa],
XM [auth aa],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth aa],
YK [auth aa],
YL [auth aa],
YM [auth aa],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth aa],
ZK [auth aa],
ZL [auth aa],
ZM [auth aa]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AJ [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT096570
Wellcome TrustUnited Kingdom110301/Z/15/Z
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Agouron InstituteUnited Kingdom--
Louis-Jeantet FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-02-07
    Changes: Structure summary
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Derived calculations