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- PDB-7pkq: Small subunit of the Chlamydomonas reinhardtii mitoribosome -

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Basic information

Entry
Database: PDB / ID: 7pkq
TitleSmall subunit of the Chlamydomonas reinhardtii mitoribosome
Components
  • (Mitochondrial ribosomal protein ...) x 3
  • 30S ribosomal protein S9, chloroplastic
  • Plastid-specific ribosomal protein 4
  • Ribosomal_S10 domain-containing protein
  • Ribosomal_S3_C domain-containing protein
  • S1 rRNA
  • S2 rRNA
  • S3 rRNA
  • S4 rRNA
  • S5 DRBM domain-containing protein
  • Unk1
  • Unk2
  • Unk3
  • Unk4
  • Unk5
  • Unk6
  • bS16m
  • bS18m
  • bS1m
  • mS105
  • mS106
  • mS107
  • mS23
  • mS26
  • mS29
  • mS31/46
  • mS33
  • mS34
  • mS35
  • mS45
  • mS45-insert
  • uS11m
  • uS12m
  • uS15m
  • uS17m
  • uS19m
  • uS2m
  • uS4m
  • uS7m,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein
  • uS8m
KeywordsRIBOSOME / Mitochondria / mitoribosome / alga
Function / homology
Function and homology information


mitochondrial small ribosomal subunit / chloroplast / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix ...mitochondrial small ribosomal subunit / chloroplast / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...: / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S19, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS10 domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein uS15c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein ...: / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS10 domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein uS15c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein uS7 domain-containing protein / Small ribosomal subunit protein uS3 C-terminal domain-containing protein / Mitochondrial ribosomal protein S16 / Mitochondrial glycoprotein / Small ribosomal subunit protein bS18c / S5 DRBM domain-containing protein / Small ribosomal subunit protein uS19c / Mitochondrial ribosomal protein S17 / Uncharacterized protein / Mitochondrial ribosomal protein S11 / Small ribosomal subunit protein mS29 / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein uS9c / Ribosomal protein S12, mitochondrial / S1 motif domain-containing protein / Uncharacterized protein / Uncharacterized protein / : / Uncharacterized protein / : / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWaltz, F. / Soufari, H. / Hashem, Y.
Funding support France, 4items
OrganizationGrant numberCountry
European Research Council (ERC)TransTryp ID:759120 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0057_MITOCROSS France
Agence Nationale de la Recherche (ANR)MITRA, ANR-16-CE11-0024-02 France
Agence Nationale de la Recherche (ANR)DAMIA, ANR-20-CE11-0021 France
CitationJournal: To Be Published
Title: The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments
Authors: Waltz, F. / Salinas-Giege, T. / Englmeier, R. / Meichel, H. / Soufari, H. / Kuhn, L. / Pfeffer, S. / Foerster, F. / Engel, B.D. / Giege, P. / Drouard, L. / Hashem, Y.
History
DepositionAug 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: mS35
C: mS45
D: mS45-insert
K: mS31/46
L: mS105
M: mS105
N: mS105
O: mS106
P: mS107
U: Unk1
V: Unk2
W: Unk3
X: Unk4
Y: Unk5
Z: Unk6
d: uS4m
f: Mitochondrial ribosomal protein S6
p: bS16m
r: bS18m
w: mS26
1: S1 rRNA
4: S4 rRNA
2: S2 rRNA
3: S3 rRNA
a: bS1m
b: uS2m
e: S5 DRBM domain-containing protein
o: uS15m
z: mS34
v: mS23
q: uS17m
l: uS12m
h: uS8m
k: uS11m
j: Ribosomal_S10 domain-containing protein
m: Mitochondrial ribosomal protein S13
n: Mitochondrial ribosomal protein S14
u: Plastid-specific ribosomal protein 4
s: uS19m
g: uS7m,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein
i: 30S ribosomal protein S9, chloroplastic
x: mS29
c: Ribosomal_S3_C domain-containing protein
y: mS33


Theoretical massNumber of molelcules
Total (without water)1,608,53844
Polymers1,608,53844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 34 types, 36 molecules BCDKLMNOPVWXYZdprwabeozvqlhkju...

#1: Protein mS35


Mass: 88892.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CST5
#2: Protein mS45


Mass: 102234.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DM91
#3: Protein mS45-insert


Mass: 36187.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#4: Protein mS31/46


Mass: 15847.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#5: Protein mS105


Mass: 28879.045 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DAY3
#6: Protein mS106


Mass: 51927.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DZV7
#7: Protein mS107


Mass: 43833.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CRX4
#9: Protein Unk2


Mass: 12953.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#10: Protein Unk3


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#11: Protein Unk4


Mass: 6911.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#12: Protein Unk5


Mass: 9209.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#13: Protein Unk6


Mass: 48613.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#14: Protein uS4m


Mass: 43497.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E198
#16: Protein bS16m


Mass: 10058.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D9S4
#17: Protein bS18m


Mass: 36901.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DDW6
#18: Protein mS26


Mass: 22474.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J4B1
#23: Protein bS1m


Mass: 26942.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IB56
#24: Protein uS2m


Mass: 53354.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXL0
#25: Protein S5 DRBM domain-containing protein


Mass: 38876.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DFB5
#26: Protein uS15m


Mass: 34706.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CQY8
#27: Protein mS34


Mass: 14287.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J254
#28: Protein mS23


Mass: 20813.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IW03
#29: Protein uS17m


Mass: 22409.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DKB4
#30: Protein uS12m


Mass: 14082.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E3V0
#31: Protein uS8m


Mass: 44616.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CNM3
#32: Protein uS11m


Mass: 23121.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DQ48
#33: Protein Ribosomal_S10 domain-containing protein


Mass: 61617.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CN25
#36: Protein Plastid-specific ribosomal protein 4


Mass: 14437.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J1A6
#37: Protein uS19m


Mass: 12951.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DHN0
#38: Protein uS7m,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein


Mass: 32755.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXT8
#39: Protein 30S ribosomal protein S9, chloroplastic


Mass: 45610.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E2Q3
#40: Protein mS29


Mass: 49635.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DXG4
#41: Protein Ribosomal_S3_C domain-containing protein


Mass: 50704.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D7R0
#42: Protein mS33


Mass: 22289.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JI15

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Protein/peptide , 1 types, 1 molecules U

#8: Protein/peptide Unk1


Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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Mitochondrial ribosomal protein ... , 3 types, 3 molecules fmn

#15: Protein Mitochondrial ribosomal protein S6


Mass: 13661.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGX6
#34: Protein Mitochondrial ribosomal protein S13


Mass: 13758.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J3J1
#35: Protein Mitochondrial ribosomal protein S14


Mass: 13009.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6P9

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RNA chain , 4 types, 4 molecules 1423

#19: RNA chain S1 rRNA


Mass: 32590.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503
#20: RNA chain S4 rRNA


Mass: 133231.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#21: RNA chain S2 rRNA


Mass: 68527.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503
#22: RNA chain S3 rRNA


Mass: 126928.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Small subunit of the Chlamydomonas reinhardtii mitochondrial ribosome
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Mitochondrion
Buffer solutionpH: 7.6
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40131 / Num. of class averages: 1 / Symmetry type: POINT

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