7PKT

Large subunit of the Chlamydomonas reinhardtii mitoribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

How to build a ribosome from RNA fragments in Chlamydomonas mitochondria.

Waltz, F.Salinas-Giege, T.Englmeier, R.Meichel, H.Soufari, H.Kuhn, L.Pfeffer, S.Forster, F.Engel, B.D.Giege, P.Drouard, L.Hashem, Y.

(2021) Nat Commun 12: 7176-7176

  • DOI: https://doi.org/10.1038/s41467-021-27200-z
  • Primary Citation of Related Structures:  
    7PKT

  • PubMed Abstract: 

    Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.


  • Organizational Affiliation

    Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L2_C domain-containing proteinA [auth a]383Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DL58 (Chlamydomonas reinhardtii)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3mB [auth b]417Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E681 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3E681
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL4mC [auth c]427Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3D422 (Chlamydomonas reinhardtii)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL5mD [auth d]216Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DYN2 (Chlamydomonas reinhardtii)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9, chloroplasticE [auth f]304Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DRF9 (Chlamydomonas reinhardtii)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L13F [auth i]277Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mG [auth j]120Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8IYH4 (Chlamydomonas reinhardtii)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinH [auth k]337Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3D8F3 (Chlamydomonas reinhardtii)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L16 domain-containing proteinI [auth l]270Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DP67 (Chlamydomonas reinhardtii)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L17,bL17mJ [auth m]183Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DXS2 (Chlamydomonas reinhardtii)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19K [auth n]312Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8I7A8 (Chlamydomonas reinhardtii)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20L [auth o]115Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mM [auth p]370Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DDN8 (Chlamydomonas reinhardtii)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mN [auth q]377Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DSG6 (Chlamydomonas reinhardtii)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L23O [auth r]226Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
KOW domain-containing protein,uL24mP [auth s]309Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DJU3 (Chlamydomonas reinhardtii)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_TL5_C domain-containing proteinQ [auth t]366Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E0K7 (Chlamydomonas reinhardtii)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
bL27mR [auth u]173Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3E880 (Chlamydomonas reinhardtii)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mS [auth v]153Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3D077 (Chlamydomonas reinhardtii)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mT [auth w]127Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L30 domain-containing proteinU [auth x]214Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DSP9 (Chlamydomonas reinhardtii)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mV [auth y]123Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JGW4 (Chlamydomonas reinhardtii)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L33W [auth z]59Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8J9C3 (Chlamydomonas reinhardtii)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
bL34mX [auth A]280Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CX36 (Chlamydomonas reinhardtii)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mY [auth B]151Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DKX8 (Chlamydomonas reinhardtii)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Plastid ribosomal protein L6Z [auth e]207Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
mL40AA [auth D]172Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3D9N2 (Chlamydomonas reinhardtii)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mL41BA [auth E]112Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8J2J1 (Chlamydomonas reinhardtii)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
mL43CA [auth F]141Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L17DA [auth G]259Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL63/57/60EA [auth I]132Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8IS96 (Chlamydomonas reinhardtii)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL59/64FA [auth J]134Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL80GA [auth K]249Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DBX4 (Chlamydomonas reinhardtii)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL87HA [auth L]206Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mIA [auth C]36Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL113JA [auth M]876Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mL114KA [auth N]455Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL115LA [auth O]688Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8J070 (Chlamydomonas reinhardtii)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL116MA [auth P]530Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DXQ3 (Chlamydomonas reinhardtii)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL117NA [auth Q]820Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL118OA [auth R]653Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL119PA [auth S]334Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3D424 (Chlamydomonas reinhardtii)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Unk1QA [auth X]31Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
PPR*RA [auth Y]172Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Unk2SA [auth Z]49Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 46
MoleculeChains LengthOrganismImage
L1 rRNATA [auth 1]162Chlamydomonas reinhardtii
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Entity ID: 47
MoleculeChains LengthOrganismImage
L2a rRNAUA [auth 2]86Chlamydomonas reinhardtii
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Entity ID: 48
MoleculeChains LengthOrganismImage
L3a rRNA (5S)VA [auth 0]75Chlamydomonas reinhardtii
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Entity ID: 49
MoleculeChains LengthOrganismImage
L3b rRNAWA [auth 3]184Chlamydomonas reinhardtii
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Entity ID: 50
MoleculeChains LengthOrganismImage
L4 rRNAXA [auth 4]118Chlamydomonas reinhardtii
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Entity ID: 51
MoleculeChains LengthOrganismImage
L5 rRNAYA [auth 5]149Chlamydomonas reinhardtii
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Entity ID: 52
MoleculeChains LengthOrganismImage
L6 rRNAZA [auth 6]136Chlamydomonas reinhardtii
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Entity ID: 53
MoleculeChains LengthOrganismImage
L7 rRNAAB [auth 7]578Chlamydomonas reinhardtii
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Entity ID: 54
MoleculeChains LengthOrganismImage
L8 rRNABB [auth 8]413Chlamydomonas reinhardtii
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

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EB [auth S]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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CB [auth y]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 3]
AD [auth 7]
BC [auth 3]
BD [auth 7]
CC [auth 3]
AC [auth 3],
AD [auth 7],
BC [auth 3],
BD [auth 7],
CC [auth 3],
CD [auth 7],
DB [auth Q],
DC [auth 3],
DD [auth 7],
EC [auth 3],
ED [auth 7],
FB [auth 1],
FC [auth 4],
FD [auth 7],
GB [auth 1],
GC [auth 4],
GD [auth 7],
HB [auth 1],
HC [auth 4],
HD [auth 7],
IB [auth 1],
IC [auth 4],
ID [auth 7],
JB [auth 1],
JC [auth 4],
JD [auth 7],
KB [auth 1],
KC [auth 4],
KD [auth 7],
LB [auth 2],
LC [auth 4],
LD [auth 7],
MB [auth 2],
MC [auth 4],
MD [auth 7],
NB [auth 2],
NC [auth 5],
ND [auth 7],
OB [auth 2],
OC [auth 5],
OD [auth 8],
PB [auth 2],
PC [auth 5],
PD [auth 8],
QB [auth 2],
QC [auth 6],
QD [auth 8],
RB [auth 2],
RC [auth 6],
RD [auth 8],
SB [auth 0],
SC [auth 6],
SD [auth 8],
TB [auth 3],
TC [auth 6],
TD [auth 8],
UB [auth 3],
UC [auth 6],
UD [auth 8],
VB [auth 3],
VC [auth 6],
WB [auth 3],
WC [auth 7],
XB [auth 3],
XC [auth 7],
YB [auth 3],
YC [auth 7],
ZB [auth 3],
ZC [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionTransTryp ID:759120
Agence Nationale de la Recherche (ANR)FranceANR-11-LABX-0057_MITOCROSS
Agence Nationale de la Recherche (ANR)FranceMITRA, ANR-16-CE11-0024-02
Agence Nationale de la Recherche (ANR)FranceDAMIA, ANR-20-CE11-0021

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release