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- PDB-6lqm: Cryo-EM structure of a pre-60S ribosomal subunit - state C -

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Basic information

Entry
Database: PDB / ID: 6lqm
TitleCryo-EM structure of a pre-60S ribosomal subunit - state C
Components
  • (60S ribosomal protein ...) x 41
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S ribosomal export protein NMD3
  • Eukaryotic translation initiation factor 6
  • Ubiquitin-60S ribosomal protein L40
  • Zinc finger protein 622
KeywordsRIBOSOME / 60S / pre-60S / pre-ribosome / human 60S / human pre-ribosome / NMD3 / human NMD3
Function / homology
Function and homology information


positive regulation of protein localization to nucleolus / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / positive regulation of RNA biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation ...positive regulation of protein localization to nucleolus / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / positive regulation of RNA biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 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 / exit from mitosis / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / TORC2 complex binding / positive regulation of kinase activity / GAIT complex / G1 to G0 transition / retinal ganglion cell axon guidance / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / regulation of reactive oxygen species metabolic process / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / negative regulation of ubiquitin protein ligase activity / regulation of glycolytic process / intrinsic apoptotic signaling pathway in response to oxidative stress / maturation of 5.8S rRNA / response to aldosterone / homeostatic process / lung morphogenesis / macrophage chemotaxis / ribosomal subunit export from nucleus / Protein hydroxylation / male meiosis I / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / preribosome, large subunit precursor / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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) / maturation of LSU-rRNA / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / ribosomal large subunit biogenesis / embryo implantation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A
Similarity search - Function
Zinc finger protein 622/Rei1/Reh1 / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / Nmd3, N-terminal / Ribosomal export protein Nmd3 / : / : / NMD3 family / NMD3 OB-fold domain / NMD3 SH3 domain ...Zinc finger protein 622/Rei1/Reh1 / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / Nmd3, N-terminal / Ribosomal export protein Nmd3 / : / : / NMD3 family / NMD3 OB-fold domain / NMD3 SH3 domain / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / : / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / zinc finger / Ribosomal protein L30/YlxQ / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14, KOW motif / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L14 / Ribosomal L37ae protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Cytoplasmic 60S subunit biogenesis factor ZNF622 / 60S ribosomal export protein NMD3 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLiang, X. / Zuo, M. / Zhang, Y. / Li, N. / Ma, C. / Dong, M. / Gao, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2020
Title: Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
Authors: Xiaomeng Liang / Mei-Qing Zuo / Yunyang Zhang / Ningning Li / Chengying Ma / Meng-Qiu Dong / Ning Gao /
Abstract: Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which ...Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
0: Zinc finger protein 622
2: 28S rRNA
3: 60S ribosomal export protein NMD3
5: 5S rRNA
6: Eukaryotic translation initiation factor 6
8: 5.8S rRNA
A: 60S ribosomal protein L10a
B: 60S ribosomal protein L3
C: 60S ribosomal protein L29
D: 60S ribosomal protein L4
E: 60S ribosomal protein L30
F: 60S ribosomal protein L34
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L35
I: 60S ribosomal protein L9
J: 60S ribosomal protein L10-like
K: 60S ribosomal protein L36
L: 60S ribosomal protein L27a
M: 60S ribosomal protein L37
N: 60S ribosomal protein L11
O: 60S ribosomal protein L38
P: 60S ribosomal protein L39
Q: 60S ribosomal protein L13
R: Ubiquitin-60S ribosomal protein L40
S: 60S ribosomal protein L14
T: 60S ribosomal protein L31
U: 60S ribosomal protein L15
V: 60S ribosomal protein L13a
W: 60S ribosomal protein L36a
X: 60S ribosomal protein L37a
Y: 60S ribosomal protein L17
Z: 60S ribosomal protein L18
a: 60S ribosomal protein L19
b: 60S ribosomal protein L18a
c: 60S ribosomal protein L21
d: 60S ribosomal protein L22
e: 60S ribosomal protein L23
f: 60S ribosomal protein L24
g: 60S ribosomal protein L23a
h: 60S ribosomal protein L26
i: 60S ribosomal protein L27
l: 60S ribosomal protein L28
m: 60S ribosomal protein L8
r: 60S ribosomal protein L5
t: 60S ribosomal protein L32
u: 60S ribosomal protein L35a
v: 60S ribosomal protein L6
w: 60S ribosomal protein L7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,729,157299
Polymers2,723,05648
Non-polymers6,101251
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, negative staining
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area473070 Å2
ΔGint-5329 kcal/mol
Surface area695290 Å2

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Components

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Protein , 4 types, 4 molecules 036R

#1: Protein Zinc finger protein 622 / / Zinc finger-like protein 9


Mass: 54357.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969S3
#3: Protein 60S ribosomal export protein NMD3 / hNMD3


Mass: 61396.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMD3, CGI-07 / Plasmid: pLVX-ACGFP1-N1 / Cell line (production host): HEK293FT / Production host: Homo sapiens (human) / References: UniProt: Q96D46
#5: Protein Eukaryotic translation initiation factor 6 / eIF-6 / B(2)GCN homolog / B4 integrin interactor / CAB / p27(BBP)


Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56537
#24: Protein Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987

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RNA chain , 3 types, 3 molecules 258

#2: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1641892.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_023363
#6: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: KY962518

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60S ribosomal protein ... , 41 types, 41 molecules ABCDEFGHIJKLMNOPQSTUVWXYZabcde...

#7: Protein 60S ribosomal protein L10a / / Large ribosomal subunit protein uL1


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906
#8: Protein 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#9: Protein 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#10: Protein 60S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#11: Protein 60S ribosomal protein L30 / / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#12: Protein 60S ribosomal protein L34 / / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#13: Protein 60S ribosomal protein L7a / / Large ribosomal subunit protein eL8


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#14: Protein 60S ribosomal protein L35 / / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#15: Protein 60S ribosomal protein L9 / / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#16: Protein 60S ribosomal protein L10-like / / Large ribosomal subunit protein uL16-like


Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#17: Protein 60S ribosomal protein L36 / / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#18: Protein 60S ribosomal protein L27a / / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#19: Protein 60S ribosomal protein L37 / / Large ribosomal subunit protein eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#20: Protein 60S ribosomal protein L11 / / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#21: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#22: Protein 60S ribosomal protein L39 / / Large ribosomal subunit protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#23: Protein 60S ribosomal protein L13 / / Large ribosomal subunit protein eL13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#25: Protein 60S ribosomal protein L14 / / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#26: Protein 60S ribosomal protein L31 / / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#27: Protein 60S ribosomal protein L15 / / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#28: Protein 60S ribosomal protein L13a / / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#29: Protein 60S ribosomal protein L36a / / Large ribosomal subunit protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#30: Protein 60S ribosomal protein L37a / / Large ribosomal subunit protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#31: Protein 60S ribosomal protein L17 / / Large ribosomal subunit protein uL22


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#32: Protein 60S ribosomal protein L18 / / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#33: Protein 60S ribosomal protein L19 / / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#34: Protein 60S ribosomal protein L18a / / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#35: Protein 60S ribosomal protein L21 / / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#36: Protein 60S ribosomal protein L22 / / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#37: Protein 60S ribosomal protein L23 / / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#38: Protein 60S ribosomal protein L24 / / Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#39: Protein 60S ribosomal protein L23a / / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#40: Protein 60S ribosomal protein L26 / / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#41: Protein 60S ribosomal protein L27 / / Large ribosomal subunit protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#42: Protein 60S ribosomal protein L28 / / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#43: Protein 60S ribosomal protein L8 / / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#44: Protein 60S ribosomal protein L5 / / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#45: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#46: Protein 60S ribosomal protein L35a / / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#47: Protein 60S ribosomal protein L6 / / Large ribosomal subunit protein eL6


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#48: Protein 60S ribosomal protein L7 / / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124

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Non-polymers , 1 types, 251 molecules

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


Mass: 24.305 Da / Num. of mol.: 251 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of a human pre-60S ribosomal subunit state - CRIBOSOME#1-#480MULTIPLE SOURCES
2Cryo-EM structure of a human pre-60S ribosomal subunit state - CCOMPLEX#1-#2, #4-#481NATURAL
360S ribosomal export protein NMD3COMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293FT / Plasmid: pLVX-ACGFP1-N1
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21707 / Symmetry type: POINT

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