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- PDB-3jd5: Cryo-EM structure of the small subunit of the mammalian mitochond... -

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Basic information

Entry
Database: PDB / ID: 3jd5
TitleCryo-EM structure of the small subunit of the mammalian mitochondrial ribosome
Components
  • (28S ribosomal protein ...) x 27
  • 28S ribosomal RNA, mitochondial
  • Aurora kinase A interacting protein 1
  • Coiled-coil-helix-coiled-coil-helix domain containing 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • unknown
KeywordsRIBOSOME / mitoribosome / mammalian 55S mitoribosome / protein synthesis / RNA-protein complex
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding ...Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / regulation of translation / kinase activity / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein domain specific binding / phosphorylation / mRNA binding / apoptotic process / nucleolus / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial ...Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / 40S ribosomal protein rpS2 (S5p), N-terminal / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 S2 signature 1. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal S11, conserved site / Ribosomal protein S17/S11 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal protein S12/S23 / Ribosomal protein S17
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / 28S ribosomal protein S15, mitochondrial / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m ...RNA / RNA (> 10) / RNA (> 100) / 28S ribosomal protein S15, mitochondrial / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS40 / Small ribosomal subunit protein bS21m / 28S ribosomal protein S29, mitochondrial / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein uS12m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein uS14m
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsKaushal, P.S. / Sharma, M.R. / Booth, T.M. / Haque, E.M. / Tung, C.S. / Sanbonmatsu, K.Y. / Spremulli, L.L. / Agrawal, R.K.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome.
Authors: Prem S Kaushal / Manjuli R Sharma / Timothy M Booth / Emdadul M Haque / Chang-Shung Tung / Karissa Y Sanbonmatsu / Linda L Spremulli / Rajendra K Agrawal /
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 ...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.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 13, 2016ID: 3J6V
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 28S ribosomal RNA, mitochondial
B: 28S ribosomal protein S2, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
E: 28S ribosomal protein S5, mitochondrial
F: 28S ribosomal protein S6, mitochondrial
G: 28S ribosomal protein S7, mitochondrial
I: 28S ribosomal protein S9, mitochondrial
J: 28S ribosomal protein S10, mitochondrial
K: 28S ribosomal protein S11, mitochondrial
L: 28S ribosomal protein S12, mitochondrial
N: 28S ribosomal protein S14, mitochondrial
O: 28S ribosomal protein S15, mitochondrial
P: 28S ribosomal protein S16, mitochondrial
Q: 28S ribosomal protein S17, mitochondrial
R: 28S ribosomal protein S18c, mitochondrial
U: 28S ribosomal protein S21, mitochondrial
a: 28S ribosomal protein S22, mitochondrial
b: 28S ribosomal protein S23, mitochondrial
c: 28S ribosomal protein S25, mitochondrial
d: 28S ribosomal protein S26, mitochondrial
e: 28S ribosomal protein S27, mitochondrial
f: 28S ribosomal protein S28, mitochondrial
g: 28S ribosomal protein S29, mitochondrial
h: 28S ribosomal protein S31, mitochondrial
i: 28S ribosomal protein S33, mitochondrial
j: 28S ribosomal protein S34, mitochondrial
k: 28S ribosomal protein S35, mitochondrial
m: Coiled-coil-helix-coiled-coil-helix domain containing 1
n: Aurora kinase A interacting protein 1
o: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
p: 28S ribosomal protein S18b, mitochondrial
s: unknown
z: unknown


Theoretical massNumber of molelcules
Total (without water)1,123,25433
Polymers1,123,25433
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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28S ribosomal protein ... , 27 types, 27 molecules BCEFGIJKLNOPQRUabcdefghijkp

#2: Protein 28S ribosomal protein S2, mitochondrial / Ribosome / MRP-S2 / S2mt


Mass: 31775.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82923
#3: Protein 28S ribosomal protein S24, mitochondrial / Ribosome / MRP-S24 / S24mt


Mass: 19111.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2M2T7
#4: Protein 28S ribosomal protein S5, mitochondrial / Ribosome / MRP-S5 / S5mt


Mass: 47956.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2KID9
#5: Protein 28S ribosomal protein S6, mitochondrial / Ribosome / MRP-S6 / S6mt


Mass: 14171.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82931
#6: Protein 28S ribosomal protein S7, mitochondrial / Ribosome / MRP-S7 / S7mt


Mass: 28179.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q3T040
#7: Protein 28S ribosomal protein S9, mitochondrial / Ribosome / MRP-S9 / S9mt


Mass: 45302.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q58DQ5
#8: Protein 28S ribosomal protein S10, mitochondrial / Ribosome / MRP-S10 / S10mt


Mass: 23069.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82670
#9: Protein 28S ribosomal protein S11, mitochondrial / Ribosome / MRP-S11 / S11mt


Mass: 20869.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82911
#10: Protein 28S ribosomal protein S12, mitochondrial / Ribosome / MRP-S12 / S12mt


Mass: 15479.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q29RU1
#11: Protein 28S ribosomal protein S14, mitochondrial / Ribosome / MRP-S14 / S14mt


Mass: 15073.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q6B860
#12: Protein 28S ribosomal protein S15, mitochondrial / Ribosome


Mass: 29245.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: E1BBB4, UniProt: P82913*PLUS
#13: Protein 28S ribosomal protein S16, mitochondrial / Ribosome / MRP-S16 / S16mt


Mass: 15157.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82915
#14: Protein 28S ribosomal protein S17, mitochondrial / Ribosome / MRP-S17 / S17mt


Mass: 14497.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82916
#15: Protein 28S ribosomal protein S18c, mitochondrial / Ribosome / MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1


Mass: 16240.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82917
#16: Protein 28S ribosomal protein S21, mitochondrial / Ribosome / MRP-S21 / S21mt


Mass: 10697.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82920
#17: Protein 28S ribosomal protein S22, mitochondrial / Ribosome / MRP-S22 / S22mt


Mass: 40720.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82649
#18: Protein 28S ribosomal protein S23, mitochondrial / Ribosome / MRP-S23 / S23mt


Mass: 21625.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2NL27
#19: Protein 28S ribosomal protein S25, mitochondrial / Ribosome / MRP-S25 / S25mt


Mass: 20085.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82669
#20: Protein 28S ribosomal protein S26, mitochondrial / Ribosome / MRP-S26 / S26mt


Mass: 23815.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q3SZ86
#21: Protein 28S ribosomal protein S27, mitochondrial / Ribosome / MRP-S27 / S27mt


Mass: 48017.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q32PI8
#22: Protein 28S ribosomal protein S28, mitochondrial / Ribosome / MRP-S28 / S28mt


Mass: 21077.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82928
#23: Protein 28S ribosomal protein S29, mitochondrial / Ribosome / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3


Mass: 45634.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82922
#24: Protein 28S ribosomal protein S31, mitochondrial / Ribosome / MRP-S31 / S31mt


Mass: 43740.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82925
#25: Protein 28S ribosomal protein S33, mitochondrial / Ribosome / MRP-S33 / S33mt


Mass: 12480.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82926
#26: Protein 28S ribosomal protein S34, mitochondrial / Ribosome / MRP-S34 / S34mt


Mass: 25880.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82929
#27: Protein 28S ribosomal protein S35, mitochondrial / Ribosome / MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt


Mass: 37129.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2YDF6
#31: Protein 28S ribosomal protein S18b, mitochondrial / Ribosome / MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2


Mass: 29217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: P82918

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Protein , 3 types, 3 molecules mno

#28: Protein Coiled-coil-helix-coiled-coil-helix domain containing 1


Mass: 13581.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2HJE8
#29: Protein Aurora kinase A interacting protein 1


Mass: 22968.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q0VCJ1
#30: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39


Mass: 60587.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2KI62

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RNA chain / Protein/peptide , 2 types, 3 molecules Asz

#1: RNA chain 28S ribosomal RNA, mitochondial /


Mass: 306932.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion
#32: Protein/peptide unknown


Mass: 1464.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion

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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 mitochondrial ribosome / Type: RIBOSOME
Buffer solutionName: 20 mM HEPES-KOH, pH 7.6, 20 mM MgCl2, 40 mM KCl, 20 mM DTT
pH: 7.6
Details: 20 mM HEPES-KOH, pH 7.6, 20 mM MgCl2, 40 mM KCl, 20 mM DTT
SpecimenConc.: 0.86 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh Quantifoil holey carbon copper grid, carbon support, glow-discharged in a plasma cleaner
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK I). / Method: flash freezing

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FS / Date: Oct 10, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Calibrated magnification: 59717 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Camera length: 800 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 100 K / Temperature (max): 105 K / Temperature (min): 80 K
Image recordingElectron dose: 9 e/Å2 / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k)

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Processing

EM software
IDNameVersionCategory
1MDFFmodel fitting
2RELION1.23D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: single particle reconstructionSingle particle analysis
Resolution: 7 Å / Num. of particles: 307556 / Nominal pixel size: 1.17 Å / Actual pixel size: 1.17 Å
Details: A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those ...Details: A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those with low cross-correlation coefficient values with the 55S reference projections - were removed.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--Flexible fitting REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-ID
15AJ3

5aj3

1
23J9M

3j9m

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms44063 20256 0 0 64319
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00167784
ELECTRON MICROSCOPYf_angle_d0.30496128
ELECTRON MICROSCOPYf_chiral_restr0.02811345
ELECTRON MICROSCOPYf_plane_restr0.0038792
ELECTRON MICROSCOPYf_dihedral_angle_d9.40139147

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