3JD5

Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome.

Kaushal, P.S.Sharma, M.R.Booth, T.M.Haque, E.M.Tung, C.S.Sanbonmatsu, K.Y.Spremulli, L.L.Agrawal, R.K.

(2014) Proc.Natl.Acad.Sci.USA 111: 7284-7289

  • DOI: 10.1073/pnas.1401657111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian ...

    The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges.


    Organizational Affiliation

    Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S2, mitochondrial
B
293Bos taurusMutation(s): 0 
Gene Names: MRPS2
Find proteins for P82923 (Bos taurus)
Go to Gene View: MRPS2
Go to UniProtKB:  P82923
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S24, mitochondrial
C
167Bos taurusMutation(s): 0 
Gene Names: MRPS24
Find proteins for Q2M2T7 (Bos taurus)
Go to Gene View: MRPS24
Go to UniProtKB:  Q2M2T7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S5, mitochondrial
E
430Bos taurusMutation(s): 0 
Gene Names: MRPS5
Find proteins for Q2KID9 (Bos taurus)
Go to Gene View: MRPS5
Go to UniProtKB:  Q2KID9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S6, mitochondrial
F
124Bos taurusMutation(s): 0 
Gene Names: MRPS6 (RPMS6)
Find proteins for P82931 (Bos taurus)
Go to Gene View: MRPS6
Go to UniProtKB:  P82931
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S7, mitochondrial
G
242Bos taurusMutation(s): 0 
Gene Names: MRPS7
Find proteins for Q3T040 (Bos taurus)
Go to Gene View: MRPS7
Go to UniProtKB:  Q3T040
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S9, mitochondrial
I
396Bos taurusMutation(s): 0 
Gene Names: MRPS9
Find proteins for Q58DQ5 (Bos taurus)
Go to Gene View: MRPS9
Go to UniProtKB:  Q58DQ5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S10, mitochondrial
J
201Bos taurusMutation(s): 0 
Gene Names: MRPS10
Find proteins for P82670 (Bos taurus)
Go to Gene View: MRPS10
Go to UniProtKB:  P82670
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S11, mitochondrial
K
197Bos taurusMutation(s): 0 
Gene Names: MRPS11
Find proteins for P82911 (Bos taurus)
Go to Gene View: MRPS11
Go to UniProtKB:  P82911
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S12, mitochondrial
L
139Bos taurusMutation(s): 0 
Gene Names: MRPS12
Find proteins for Q29RU1 (Bos taurus)
Go to Gene View: MRPS12
Go to UniProtKB:  Q29RU1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S14, mitochondrial
N
128Bos taurusMutation(s): 0 
Gene Names: MRPS14
Find proteins for Q6B860 (Bos taurus)
Go to Gene View: MRPS14
Go to UniProtKB:  Q6B860
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S15, mitochondrial
O
256Bos taurusMutation(s): 0 
Gene Names: MRPS15 (RPMS15)
Find proteins for P82913 (Bos taurus)
Go to Gene View: MRPS15
Go to UniProtKB:  P82913
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S16, mitochondrial
P
135Bos taurusMutation(s): 0 
Gene Names: MRPS16 (RPMS16)
Find proteins for P82915 (Bos taurus)
Go to Gene View: MRPS16
Go to UniProtKB:  P82915
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S17, mitochondrial
Q
130Bos taurusMutation(s): 0 
Gene Names: MRPS17 (RPMS17)
Find proteins for P82916 (Bos taurus)
Go to Gene View: MRPS17
Go to UniProtKB:  P82916
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S18c, mitochondrial
R
143Bos taurusMutation(s): 0 
Gene Names: MRPS18C
Find proteins for P82917 (Bos taurus)
Go to Gene View: MRPS18C
Go to UniProtKB:  P82917
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S21, mitochondrial
U
87Bos taurusMutation(s): 0 
Gene Names: MRPS21 (RPMS21)
Find proteins for P82920 (Bos taurus)
Go to Gene View: MRPS21
Go to UniProtKB:  P82920
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S22, mitochondrial
a
359Bos taurusMutation(s): 0 
Gene Names: MRPS22
Find proteins for P82649 (Bos taurus)
Go to Gene View: MRPS22
Go to UniProtKB:  P82649
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S23, mitochondrial
b
190Bos taurusMutation(s): 0 
Gene Names: MRPS23
Find proteins for Q2NL27 (Bos taurus)
Go to Gene View: MRPS23
Go to UniProtKB:  Q2NL27
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S25, mitochondrial
c
173Bos taurusMutation(s): 0 
Gene Names: MRPS25 (RPMS25)
Find proteins for P82669 (Bos taurus)
Go to Gene View: MRPS25
Go to UniProtKB:  P82669
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S26, mitochondrial
d
205Bos taurusMutation(s): 0 
Gene Names: MRPS26
Find proteins for Q3SZ86 (Bos taurus)
Go to Gene View: MRPS26
Go to UniProtKB:  Q3SZ86
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S27, mitochondrial
e
415Bos taurusMutation(s): 0 
Gene Names: MRPS27
Find proteins for Q32PI8 (Bos taurus)
Go to Gene View: MRPS27
Go to UniProtKB:  Q32PI8
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S28, mitochondrial
f
189Bos taurusMutation(s): 0 
Gene Names: MRPS28
Find proteins for P82928 (Bos taurus)
Go to Gene View: MRPS28
Go to UniProtKB:  P82928
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S29, mitochondrial
g
397Bos taurusMutation(s): 0 
Gene Names: DAP3 (MRPS29)
Find proteins for P82922 (Bos taurus)
Go to Gene View: DAP3
Go to UniProtKB:  P82922
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S31, mitochondrial
h
386Bos taurusMutation(s): 0 
Gene Names: MRPS31
Find proteins for P82925 (Bos taurus)
Go to Gene View: MRPS31
Go to UniProtKB:  P82925
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S33, mitochondrial
i
106Bos taurusMutation(s): 0 
Gene Names: MRPS33
Find proteins for P82926 (Bos taurus)
Go to Gene View: MRPS33
Go to UniProtKB:  P82926
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S34, mitochondrial
j
218Bos taurusMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82929 (Bos taurus)
Go to Gene View: MRPS34
Go to UniProtKB:  P82929
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S35, mitochondrial
k
325Bos taurusMutation(s): 0 
Gene Names: MRPS35 (MRPS28)
Find proteins for Q2YDF6 (Bos taurus)
Go to Gene View: MRPS35
Go to UniProtKB:  Q2YDF6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Coiled-coil-helix-coiled-coil-helix domain containing 1
m
118Bos taurusMutation(s): 0 
Gene Names: CHCHD1
Find proteins for Q2HJE8 (Bos taurus)
Go to Gene View: CHCHD1
Go to UniProtKB:  Q2HJE8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A interacting protein 1
n
199Bos taurusMutation(s): 0 
Gene Names: AURKAIP1
Find proteins for Q0VCJ1 (Bos taurus)
Go to Gene View: AURKAIP1
Go to UniProtKB:  Q0VCJ1
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Pentatricopeptide repeat domain-containing protein 3, mitochondrial
o
575Bos taurusMutation(s): 0 
Gene Names: PTCD3 (MRPS39)
Find proteins for Q2KI62 (Bos taurus)
Go to Gene View: PTCD3
Go to UniProtKB:  Q2KI62
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S18b, mitochondrial
p
258Bos taurusMutation(s): 0 
Gene Names: MRPS18B
Find proteins for P82918 (Bos taurus)
Go to Gene View: MRPS18B
Go to UniProtKB:  P82918
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
unknown
s, z
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNA, mitochondialA955Bos taurus
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
o, s, z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection