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- PDB-2ftc: Structural Model for the Large Subunit of the Mammalian Mitochond... -

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Basic information

Entry
Database: PDB / ID: 2ftc
TitleStructural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome
Components
  • (39S ribosomal protein ...) x 5
  • (Mitochondrial 39S ribosomal protein ...) x 2
  • (Mitochondrial ribosomal protein ...) x 8
  • MRPL20 protein
  • Mitochondrial 16S ribosomal RNA
KeywordsRIBOSOME / MITOCHONDRIAL RIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOMAL RNA
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / maturation of LSU-rRNA / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / maturation of LSU-rRNA / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / mitochondrial inner membrane / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Ribosomal protein L1, mitochondrial / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L11, bacterial-type ...Ribosomal protein L1, mitochondrial / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / 50S ribosomal protein uL4 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L1, mitochondrial / 39S ribosomal protein L34, mitochondrial / 39S ribosomal protein L19, mitochondrial / Large ribosomal subunit protein uL2m / 39S ribosomal protein L20, mitochondrial ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L1, mitochondrial / 39S ribosomal protein L34, mitochondrial / 39S ribosomal protein L19, mitochondrial / Large ribosomal subunit protein uL2m / 39S ribosomal protein L20, mitochondrial / Large ribosomal subunit protein uL11m / 39S ribosomal protein L27, mitochondrial / 39S ribosomal protein L4, mitochondrial / Large ribosomal subunit protein uL24m / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L33, mitochondrial / Large ribosomal subunit protein uL22m / 39S ribosomal protein L16, mitochondrial / Large ribosomal subunit protein bL17m / 39S ribosomal protein L3, mitochondrial / 39S ribosomal protein L12, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.1 Å
AuthorsMears, J.A. / Sharma, M.R. / Gutell, R.R. / Richardson, P.E. / Agrawal, R.K. / Harvey, S.C.
CitationJournal: J Mol Biol / Year: 2006
Title: A structural model for the large subunit of the mammalian mitochondrial ribosome.
Authors: Jason A Mears / Manjuli R Sharma / Robin R Gutell / Amanda S McCook / Paul E Richardson / Thomas R Caulfield / Rajendra K Agrawal / Stephen C Harvey /
Abstract: Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of ...Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 999SEQUENCE SINCE THE SEQUENCE OF THE HUMAN AND BOVINE MITOCHONDRIAL PROTEINS ARE ESSENTIALLY ...SEQUENCE SINCE THE SEQUENCE OF THE HUMAN AND BOVINE MITOCHONDRIAL PROTEINS ARE ESSENTIALLY IDENTICAL, THE SEQUENCE DATABASE REFERENCE FOR THE PROTEINS USED IN MODELLING FOR THIS DEPOSITION WAS FROM A HUNAN SOURCE (AND NOT BOVINE).THUS THE REFERENCE USED FOR THE PROTEIN CHAINS ARE LISTED BELOW CHAIN ID DATABASE REFERENCE A GB AAH14356 B GB NP_057034 C SWS RM03_HUMAN D GB NP_666499 E GB NP_963900 F GB NP_963900 G SWS RM11_HUMAN H SWS RM13_HUMAN I GB AAH01040 J GB AAH12306 K SWS RM19_HUMAN L GB AAH59945 M GB NP_054899 N GB CAI16343 O SWS RM27_HUMAN P GB NP_004882 Q SWS RM34_HUMAN

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Assembly

Deposited unit
R: Mitochondrial 16S ribosomal RNA
A: Mitochondrial ribosomal protein L1
B: mitochondrial ribosomal protein L2
C: Mitochondrial 39S ribosomal protein L3
D: mitochondrial ribosomal protein L4 isoform a
E: 39S ribosomal protein L12, mitochondrial
F: 39S ribosomal protein L12, mitochondrial
G: 39S ribosomal protein L11, mitochondrial
H: 39S ribosomal protein L13, mitochondrial
I: Mitochondrial ribosomal protein L16
J: Mitochondrial ribosomal protein L17
K: 39S ribosomal protein L19, mitochondrial
L: MRPL20 protein
M: mitochondrial ribosomal protein L22 isoform a
N: mitochondrial ribosomal protein L24
O: Mitochondrial 39S ribosomal protein L27
P: mitochondrial ribosomal protein L33 isoform a
Q: 39S ribosomal protein L34, mitochondrial


Theoretical massNumber of molelcules
Total (without water)739,18918
Polymers739,18918
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mitochondrial ribosomal protein ... , 8 types, 8 molecules ABDIJMNP

#2: Protein Mitochondrial ribosomal protein L1 / Coordinate model: Cα atoms only


Mass: 21224.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A6QPQ5*PLUS
#3: Protein mitochondrial ribosomal protein L2 / Coordinate model: Cα atoms only


Mass: 14442.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA12*PLUS
#5: Protein mitochondrial ribosomal protein L4 isoform a / Coordinate model: Cα atoms only


Mass: 19707.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32PI6*PLUS
#9: Protein Mitochondrial ribosomal protein L16 / Coordinate model: Cα atoms only


Mass: 13107.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0J3*PLUS
#10: Protein Mitochondrial ribosomal protein L17 / Coordinate model: Cα atoms only


Mass: 13682.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0L3*PLUS
#13: Protein mitochondrial ribosomal protein L22 isoform a / Coordinate model: Cα atoms only


Mass: 12914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZX5*PLUS
#14: Protein mitochondrial ribosomal protein L24 / Coordinate model: Cα atoms only


Mass: 11010.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYS0*PLUS
#16: Protein mitochondrial ribosomal protein L33 isoform a / Coordinate model: Cα atoms only


Mass: 6092.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZ47*PLUS

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Mitochondrial 39S ribosomal protein ... , 2 types, 2 molecules CO

#4: Protein Mitochondrial 39S ribosomal protein L3 / L3mt / MRP-L3 / Coordinate model: Cα atoms only


Mass: 23396.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBX6*PLUS
#15: Protein Mitochondrial 39S ribosomal protein L27 / L27mt / MRP-L27 / Coordinate model: Cα atoms only


Mass: 7520.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32PC3*PLUS

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39S ribosomal protein ... , 5 types, 6 molecules EFGHKQ

#6: Protein 39S ribosomal protein L12, mitochondrial / Ribosome / L12mt / MRP-L12 / Coordinate model: Cα atoms only


Mass: 14831.392 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q7YR75
#7: Protein 39S ribosomal protein L11, mitochondrial / Ribosome / L11mt / MRP-L11 / Coordinate model: Cα atoms only


Mass: 15606.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2YDI0*PLUS
#8: Protein 39S ribosomal protein L13, mitochondrial / Ribosome / L13mt / MRP-L13 / Coordinate model: Cα atoms only


Mass: 16958.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYS1*PLUS
#11: Protein 39S ribosomal protein L19, mitochondrial / Ribosome / L19mt / MRP-L19 / MRP-L15 / Coordinate model: Cα atoms only


Mass: 11098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2HJI0*PLUS
#17: Protein/peptide 39S ribosomal protein L34, mitochondrial / Ribosome / L34mt / MRP-L34 / Coordinate model: Cα atoms only


Mass: 4485.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A8NN94*PLUS

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RNA chain / Protein , 2 types, 2 molecules RL

#12: Protein MRPL20 protein / Coordinate model: Cα atoms only


Mass: 14125.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TBR2*PLUS
#1: RNA chain Mitochondrial 16S ribosomal RNA / Coordinate model: P atoms only


Mass: 504151.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: GenBank: 56411146

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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: Mammalian Mitochondrial Ribosome Large Subunit / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4600 nm / Nominal defocus min: 1200 nm
Image scansNum. digital images: 194 / Scanner model: ZEISS SCAI

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Processing

SoftwareName: YAMMP / Classification: refinement
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 12.1 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11GIY

1giy
PDB Unreleased entry

11GIY1PDBexperimental model
21JJ211JJ22PDBexperimental model
31NKW11NKW3PDBexperimental model
41PNU

1pnu
PDB Unreleased entry

11PNU4PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 1443 0 0 3536

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