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- PDB-6n8n: Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit -

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Open data

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Basic information

Entry	Database: PDB / ID: 6n8n
Title	Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit
Components	(60S ribosomal protein ...) x 38 5.8S rRNA5.8S ribosomal RNA 5S rRNA5S ribosomal RNA 60S ribosomal export protein NMD3 Eukaryotic translation initiation factor 6 Large subunit GTPase 1 Ribosomal Protein uL1 Ribosomal protein L12 Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA Tyrosine-protein phosphatase YVH1 Ubiquitin-60S ribosomal protein L40
Keywords	RIBOSOME / ribosome biogenesis / Nmd3 / peptidyl transferase center
Function / homology	Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal export protein Nmd3 / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L35A superfamily / Ubiquitin family ...Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal export protein Nmd3 / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L35A superfamily / Ubiquitin family / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L23 / Ribosomal protein L36e domain superfamily / Ribosomal L15 / Ribosomal protein L21e / Ribosomal L40e family / Ribosomal protein L44 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Dual specificity phosphatase, catalytic domain / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein L6 / Ribosomal protein L30p/L7e / Ribosomal protein L3 / Ribosomal protein L38e superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L6e / Ribosomal protein L4 domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Dual specificity phosphatase / Ribosomal protein L15e core domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L13 superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L32e superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L7, eukaryotic/archaeal / Protein-tyrosine phosphatase-like / Ribosomal protein L19, eukaryotic / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L36e / Ribosomal protein L31e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L7Ae signature. / Ribosomal protein L31e signature. / Ribosomal protein L24 signature. / Ribosomal protein L27e signature. / Ribosomal protein L18e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L37e signature. / Ribosomal protein L6e signature. / Ribosomal protein L24e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L1e signature. / Ribosomal protein L13 signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L6 signature 2. / Ribosomal protein L34e signature. / Ribosomal protein L21e signature. / Ribosomal protein L32e signature. / Translesion Synthesis by POLH / Translesion synthesis by POLK / AUF1 (hnRNP D0) binds and destabilizes mRNA / ABC-family proteins mediated transport / SCF(Skp2)-mediated degradation of p27/p21 / SCF-beta-TrCP mediated degradation of Emi1 / L13a-mediated translational silencing of Ceruloplasmin expression Function and homology information
Specimen source	Saccharomyces cerevisiae (baker's yeast)
Method	ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
Authors	Zhou, Y. / Musalgaonkar, S. / Johnson, A.W. / Taylor, D.W.
Citation	Journal: Nat Commun / Year: 2019 Title: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Authors: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor
Validation Report	Summary Full report About validation report
Date	Deposition: Nov 29, 2018 / Release: Mar 13, 2019

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Structure visualization

Movie	Deposited structure unit Imaged by Jmol Download Superimposition on EM map EMDB-0373 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmcif format	6n8n.cif.gz / Display in browser / Tree view / PDBx/mmCIF dictionary
PDB format	pdb6n8n.ent.gz / Display in browser / PDB Contents Guide
PDBML Plus	6n8n-add.xml.gz / Display in browser*PLUS
Others	Other downloads

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PDB pages	PDBj / RCSB PDB / PDBe / NCBI

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Related structure data

Related structure data	CM0373 C0369 C0370 C0371 C0372 C0374 C6n8j C6n8k C6n8l C6n8m C6n8o C: citing same article M: map data used to model this data
Similar-shape strucutres	6n8o 6n8m 0373 5771 5796 2847 Search similar-shape structures by Omokage search Omokage search

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Assembly

Deposited unit

A: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA

B: 5S rRNA

C: 5.8S rRNA

Y: Tyrosine-protein phosphatase YVH1

X: Eukaryotic translation initiation factor 6

W: Large subunit GTPase 1

V: 60S ribosomal export protein NMD3

D: 60S ribosomal protein L2-A

E: 60S ribosomal protein L3

F: 60S ribosomal protein L4-A

G: 60S ribosomal protein L5

H: 60S ribosomal protein L6-A

I: 60S ribosomal protein L7-A

J: 60S ribosomal protein L8-A

K: 60S ribosomal protein L9-A

M: 60S ribosomal protein L11-A

N: 60S ribosomal protein L13-A

O: 60S ribosomal protein L14-A

Q: 60S ribosomal protein L42-A

R: 60S ribosomal protein L43-A

S: Ribosomal Protein uL1

a: 60S ribosomal protein L15-A

b: 60S ribosomal protein L16-A

c: 60S ribosomal protein L17-A

d: 60S ribosomal protein L18-A

e: 60S ribosomal protein L19-A

f: 60S ribosomal protein L20-A

g: 60S ribosomal protein L21-A

h: 60S ribosomal protein L22-A

i: 60S ribosomal protein L23-A

j: 60S ribosomal protein L24-A

k: 60S ribosomal protein L25

l: 60S ribosomal protein L26-A

m: 60S ribosomal protein L27-A

n: 60S ribosomal protein L28

o: 60S ribosomal protein L29

p: 60S ribosomal protein L30

q: 60S ribosomal protein L31-A

r: 60S ribosomal protein L32

s: 60S ribosomal protein L33-A

t: 60S ribosomal protein L34-A

u: 60S ribosomal protein L35-A

v: 60S ribosomal protein L36-A

w: 60S ribosomal protein L37-A

x: 60S ribosomal protein L38

y: 60S ribosomal protein L39

z: Ubiquitin-60S ribosomal protein L40

L: Ribosomal protein L12

2.14 MDa, 48 polymers
Search similar-shape structures of this assembly by Omokage search (details)

idetical with deposited unit
defined by author
Evidence: mass spectrometry

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain	Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA Mass: 1097493.875 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: REF: 831416132
#2: RNA chain	5S rRNA / 5S ribosomal RNA Mass: 38951.105 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: GenBank: 1329886537
#3: RNA chain	5.8S rRNA / 5.8S ribosomal RNA Mass: 50682.922 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: GenBank: 1489318609

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Protein/peptide , 7 types, 7 molecules YXWVSzL

#4: Protein/peptide	Tyrosine-protein phosphatase YVH1 / PTPase YVH1 Mass: 41242.121 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02256, protein-tyrosine-phosphatase
#5: Protein/peptide	Eukaryotic translation initiation factor 6 / eIF-6 Mass: 26476.605 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#6: Protein/peptide	Large subunit GTPase 1 Mass: 72838.445 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P53145, Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides
#7: Protein/peptide	60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3 Mass: 59167.047 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38861
#21: Protein/peptide	Ribosomal Protein uL1 / Mass: 18485.723 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c
#47: Protein/peptide	Ubiquitin-60S ribosomal protein L40 Mass: 14583.077 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CH08
#48: Protein/peptide	Ribosomal protein L12 / Mass: 15951.983 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c

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60S ribosomal protein ... , 38 types, 38 molecules DEFGHIJKMNOQRabcdefghijklmnopq...

#8: Protein/peptide	60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6 Mass: 27463.574 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#9: Protein/peptide	60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1 Mass: 43850.793 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P14126
#10: Protein/peptide	60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2 Mass: 39159.125 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P10664
#11: Protein/peptide	60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3 Mass: 33764.828 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P26321
#12: Protein/peptide	60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16 Mass: 20000.564 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#13: Protein/peptide	60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8 Mass: 27686.281 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05737
#14: Protein/peptide	60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5 Mass: 28175.820 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P17076
#15: Protein/peptide	60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11 Mass: 21605.061 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05738
#16: Protein/peptide	60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22 Mass: 19755.691 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#17: Protein/peptide	60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A Mass: 22604.164 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#18: Protein/peptide	60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A Mass: 15195.066 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P36105
#19: Protein/peptide	60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44 Mass: 12246.658 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#20: Protein/peptide	60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35 Mass: 10112.952 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX25
#22: Protein/peptide	60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18 Mass: 24482.357 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05748
#23: Protein/peptide	60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15 Mass: 22247.227 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P26784
#24: Protein/peptide	60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17 Mass: 20589.518 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05740
#25: Protein/peptide	60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28 Mass: 20609.252 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#26: Protein/peptide	60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14 Mass: 21762.316 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#27: Protein/peptide	60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A Mass: 20478.852 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#28: Protein/peptide	60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A Mass: 18279.266 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#29: Protein/peptide	60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31 Mass: 13711.359 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05749
#30: Protein/peptide	60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32 Mass: 14493.950 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#31: Protein/peptide	60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21 Mass: 17661.717 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P04449
#32: Protein/peptide	60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42' Mass: 15787.612 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P04456
#33: Protein/peptide	60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33 Mass: 14265.784 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05743
#34: Protein/peptide	60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A Mass: 15568.360 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#35: Protein/peptide	60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24 Mass: 16761.666 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P02406
#36: Protein/peptide	60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43 Mass: 6691.884 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05747
#37: Protein/peptide	60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38 Mass: 11430.364 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P14120
#38: Protein/peptide	60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28 Mass: 12980.158 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#39: Protein/peptide	60S ribosomal protein L32 / / Large ribosomal subunit protein eL32 Mass: 14809.441 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38061
#40: Protein/peptide	60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37 Mass: 12177.130 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05744
#41: Protein/peptide	60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A Mass: 13673.196 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P87262
#42: Protein/peptide	60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A Mass: 13942.640 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#43: Protein/peptide	60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39 Mass: 11151.259 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05745
#44: Protein/peptide	60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55 Mass: 9877.395 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P49166
#45: Protein/peptide	60S ribosomal protein L38 / / Large ribosomal subunit protein eL38 Mass: 8845.561 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P49167
#46: Protein/peptide	60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40 Mass: 6358.640 Da / Num. of mol.: 1 Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P04650

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Experimental details

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Lsg1-engaged (LE) pre-60S ribosomal subunit / Type: RIBOSOME Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 Source: NATURAL
Molecular weight	Units: MEGADALTONS / Experimental value: NO
Source (natural)	Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Details: unspecified
Vitrification	Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Microscope model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holder	Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording	Average exposure time: 6 sec. / Electron dose: 40 e/Å² / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scans	Movie frames/image: 20

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Processing

EM software

ID	Name	Category
2	Leginon	image acquisition
4	RELION	CTF correction
7	Coot	model fitting
9	PHENIX	model refinement
13	RELION	3D reconstruction

CTF correction

Type: PHASE FLIPPING ONLY

Symmetry

Point symmetry: C1

3D reconstruction

Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 54188 / Symmetry type: POINT

Atomic model building

Ref protocol: RIGID BODY FIT / Ref space: REAL

Atomic model building

PDB-ID: 5T62

5t62

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RNA chain , 3 types, 3 molecules ABC

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Protein/peptide , 7 types, 7 molecules YXWVSzL

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60S ribosomal protein ... , 38 types, 38 molecules DEFGHIJKMNOQRabcdefghijklmnopq...

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-RNA chain , 3 types, 3 molecules ABC

-Protein/peptide , 7 types, 7 molecules YXWVSzL

+60S ribosomal protein ... , 38 types, 38 molecules DEFGHIJKMNOQRabcdefghijklmnopq...

-Experimental details

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-Electron microscopy imaging

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RNA chain , 3 types, 3 molecules ABC

-
Protein/peptide , 7 types, 7 molecules YXWVSzL

+
60S ribosomal protein ... , 38 types, 38 molecules DEFGHIJKMNOQRabcdefghijklmnopq...

-
Experimental details

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Experiment

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Sample preparation

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Electron microscopy imaging

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Processing

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About Yorodumi

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