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- PDB-3j7o: Structure of the mammalian 60S ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 3j7o
TitleStructure of the mammalian 60S ribosomal subunit
Components
  • (Ribosomal protein ...) x 42
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / mammalian
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation at presynapse / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation ...L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation at presynapse / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / organelle membrane / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-RNA complex assembly / cytosolic ribosome / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / modification-dependent protein catabolic process / rRNA processing / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / presynapse / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / intracellular membrane-bounded organelle / mRNA binding / glutamatergic synapse / ubiquitin protein ligase binding / synapse / nucleolus / endoplasmic reticulum / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily ...Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal protein L18e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L39e / Ribosomal protein L14e domain / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L14 / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14, KOW motif / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL15 / Uncharacterized protein / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL18 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL15 / Uncharacterized protein / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL20 / Ribosomal protein L23/L25 N-terminal domain-containing protein / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34 / : / Uncharacterized protein / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL24 / Ribosomal protein L15 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L13 / : / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL18
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVoorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S.
CitationJournal: Cell / Year: 2014
Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde /
Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 3, 2014ID: 3J71, 4W1Z, 4W20
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
SupersessionDec 10, 2014ID: 4W1Z, 4W20
Revision 1.2Dec 10, 2014Group: Other
Revision 1.3Dec 17, 2014Group: Other
Revision 1.4Jul 18, 2018Group: Advisory / Data collection
Category: em_image_scans / em_software / pdbx_database_PDB_obs_spr
Item: _em_software.image_processing_id / _em_software.name / _pdbx_database_PDB_obs_spr.replace_pdb_id

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Structure visualization

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Assembly

Deposited unit
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
A: Ribosomal protein uL2
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
L: Ribosomal protein eL13
M: Ribosomal protein eL14
N: Ribosomal protein eL15
O: Ribosomal protein uL13
P: Ribosomal protein uL22
Q: Ribosomal protein eL18
R: Ribosomal protein eL19
S: Ribosomal protein eL20
T: Ribosomal protein eL21
U: Ribosomal protein eL22
V: Ribosomal protein uL14
W: Ribosomal protein eL24
X: Ribosomal protein uL23
Y: Ribosomal protein uL24
Z: Ribosomal protein eL27
a: Ribosomal protein uL15
b: Ribosomal protein eL29
c: Ribosomal protein eL30
d: Ribosomal protein eL31
e: Ribosomal protein eL32
f: Ribosomal protein eL33
g: Ribosomal protein eL34
h: Ribosomal protein uL29
i: Ribosomal protein eL36
j: Ribosomal protein eL37
k: Ribosomal protein eL38
l: Ribosomal protein eL39
m: Ribosomal protein eL40
n: Ribosomal protein eL41
o: Ribosomal protein eL42
p: Ribosomal protein eL43
r: Ribosomal protein eL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,090,573178
Polymers2,087,21845
Non-polymers3,356133
Water00
1


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

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Components

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RNA chain , 3 types, 3 molecules 578

#1: RNA chain 28S ribosomal RNA


Mass: 1187230.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#2: RNA chain 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#3: RNA chain 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

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Ribosomal protein ... , 42 types, 42 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein Ribosomal protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z567
#5: Protein Ribosomal protein uL3


Mass: 44759.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#6: Protein Ribosomal protein uL4


Mass: 41635.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#7: Protein Ribosomal protein uL18


Mass: 34417.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1S530
#8: Protein Ribosomal protein eL6


Mass: 27052.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#9: Protein Ribosomal protein uL30


Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#10: Protein Ribosomal protein eL8


Mass: 30166.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LVI8
#11: Protein Ribosomal protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LP78
#12: Protein Ribosomal protein uL16


Mass: 24465.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#13: Protein Ribosomal protein uL5


Mass: 20248.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29205
#14: Protein Ribosomal protein eL13


Mass: 24365.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LSD3
#15: Protein Ribosomal protein eL14


Mass: 23383.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU3
#16: Protein Ribosomal protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LK33
#17: Protein Ribosomal protein uL13


Mass: 23765.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RI01
#18: Protein Ribosomal protein uL22


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#19: Protein Ribosomal protein eL18


Mass: 21588.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3L6F1, UniProt: Q95342*PLUS
#20: Protein Ribosomal protein eL19


Mass: 23567.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z546
#21: Protein Ribosomal protein eL20


Mass: 26103.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1S935
#22: Protein Ribosomal protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RTJ9, UniProt: P49666*PLUS
#23: Protein Ribosomal protein eL22


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P67985
#24: Protein Ribosomal protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62831
#25: Protein Ribosomal protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#26: Protein Ribosomal protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z522
#27: Protein Ribosomal protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3L7Y1
#28: Protein Ribosomal protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU5
#29: Protein Ribosomal protein uL15


Mass: 16631.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RGC0
#30: Protein Ribosomal protein eL29


Mass: 17545.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q95281
#31: Protein Ribosomal protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z554
#32: Protein Ribosomal protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62901
#33: Protein Ribosomal protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAT0
#34: Protein Ribosomal protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5Q8
#35: Protein Ribosomal protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5B9, UniProt: Q29223*PLUS
#36: Protein Ribosomal protein uL29


Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29361
#37: Protein Ribosomal protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5K6
#38: Protein Ribosomal protein eL37


Mass: 10102.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#39: Protein Ribosomal protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z568
#40: Protein Ribosomal protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: K7GP63
#41: Protein Ribosomal protein eL40


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63053
#42: Protein/peptide Ribosomal protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#43: Protein Ribosomal protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P83884
#44: Protein Ribosomal protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#45: Protein Ribosomal protein eL28


Mass: 14301.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

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Non-polymers , 2 types, 133 molecules

#46: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 130 / Source method: obtained synthetically / Formula: Mg
#47: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: The 60S ribosomal subunit purified from porcine pancreas
Type: RIBOSOME
Buffer solutionName: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
pH: 7.5
Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K
Details: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Details: Back-thinned
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2REFMACmodel fitting
3RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particle / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80019 / Nominal pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingB value: 37 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor and FSC / Details: METHOD--Maximum likelihood
Atomic model building
IDPDB-ID 3D fitting-ID
13J3B

3j3b
PDB Unreleased entry

1
23J3F

3j3f
PDB Unreleased entry

1
RefinementResolution: 3.5→268 Å / Cor.coef. Fo:Fc: 0.856 / SU B: 22.493 / SU ML: 0.34 / σ(F): 0 / ESU R: 0.873
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.2823 722418 -
obs0.2823 -100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 0 Å2 / Biso mean: 48.645 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.22 Å2-1.11 Å2
2---1.22 Å20.01 Å2
3---1.16 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.014150793
ELECTRON MICROSCOPYr_bond_other_d0.0050.0293579
ELECTRON MICROSCOPYr_angle_refined_deg1.9161.5218388
ELECTRON MICROSCOPYr_angle_other_deg1.6213219530
ELECTRON MICROSCOPYr_dihedral_angle_1_deg28.5197.0418037
ELECTRON MICROSCOPYr_dihedral_angle_2_deg38.91220.9442299
ELECTRON MICROSCOPYr_dihedral_angle_3_deg22.7031510642
ELECTRON MICROSCOPYr_dihedral_angle_4_deg23.16115709
ELECTRON MICROSCOPYr_chiral_restr0.6150.21824826
ELECTRON MICROSCOPYr_gen_planes_refined0.020.02105984
ELECTRON MICROSCOPYr_gen_planes_other0.0050.0234523
ELECTRON MICROSCOPYr_mcbond_it1.8144.03225785
ELECTRON MICROSCOPYr_mcbond_other1.8134.03225784
ELECTRON MICROSCOPYr_mcangle_it3.2146.03732156
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.406 53450 -
obs--100 %

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