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- PDB-8inf: human nuclear pre-60S ribosomal particle - State F' -

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Entry
Database: PDB / ID: 8inf
Titlehuman nuclear pre-60S ribosomal particle - State F'
Components
  • (60S ribosomal protein ...) x 41
  • (Ribosome biogenesis protein ...) x 2
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Eukaryotic translation initiation factor 6
  • G Protein Nucleolar 2
  • GTP-binding protein 4
  • Internal Transcribed Spacer 2
  • Leydig cell tumor 10 kDa protein homolog
  • MKI67 FHA domain-interacting nucleolar phosphoprotein
  • Pescadillo homolog
  • Probable ribosome biogenesis protein RLP24
  • Protein LLP homolog
  • Protein SDA1 homolog
  • Ribosomal L1 domain-containing protein 1
  • Translation machinery-associated protein 16
  • Uncharacterized protein C11orf98
  • Zinc finger protein 593
  • mRNA turnover protein 4 homolog
KeywordsRIBOSOME / GNL2 / nuclear / pre-60S
Function / homology
Function and homology information


protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of G2/M transition of mitotic cell cycle / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / positive regulation of protein K63-linked deubiquitination / ribosomal protein import into nucleus / blastocyst formation / protein-DNA complex disassembly / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / protein localization to nucleolus / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of glycolytic process / middle ear morphogenesis / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / regulation of aerobic respiration / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / homeostatic process / negative regulation of DNA replication / rRNA metabolic process / positive regulation of dendritic spine development / macrophage chemotaxis / negative regulation of signal transduction by p53 class mediator / lung morphogenesis / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / regulation of protein phosphorylation / positive regulation of natural killer cell proliferation / Protein hydroxylation / preribosome, large subunit precursor / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / rRNA transcription / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / ribosomal large subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of protein binding / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / protein targeting / negative regulation of protein-containing complex assembly / ribosomal subunit export from nucleus / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / translation initiation factor activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / embryo implantation / cytosolic ribosome / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interleukin-4 / ossification / negative regulation of cell migration / assembly of large subunit precursor of preribosome / positive regulation of translation / regulation of signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis
Similarity search - Function
Uncharacterized protein C11orf98 / Family of unknown function (DUF5564) / Uncharacterised protein family UPF0390 / Protein of unknown function (DUF2462) / Translation machinery-associated protein 16 / Tma16 superfamily / Translation machinery-associated protein 16 / SDA1 domain / Uncharacterised domain NUC130/133, N-terminal / Sda1 ...Uncharacterized protein C11orf98 / Family of unknown function (DUF5564) / Uncharacterised protein family UPF0390 / Protein of unknown function (DUF2462) / Translation machinery-associated protein 16 / Tma16 superfamily / Translation machinery-associated protein 16 / SDA1 domain / Uncharacterised domain NUC130/133, N-terminal / Sda1 / : / SDA1, conserved domain / SDA1, HEAT repeat / SDA1, C-terminal / MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / Learning associated protein 18-like / LLP homolog / : / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / : / Pescadillo / Pescadillo N-terminus / Ribosomal biogenesis NSA2 family / GTP-binding protein, orthogonal bundle domain superfamily / : / Ribosome assembly factor Mrt4 / : / BRCT domain / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / GTP binding domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / breast cancer carboxy-terminal domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e 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 L1, 3-layer alpha/beta-sandwich / Ribosomal protein L19, eukaryotic / : / BRCT domain profile. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / BRCT domain / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / :
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein C11orf98 / Zinc finger protein 593 ...GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein C11orf98 / Zinc finger protein 593 / Pescadillo homolog / Ribosomal L1 domain-containing protein 1 / Ribosome biogenesis protein NSA2 homolog / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL11 / 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 / Large ribosomal subunit protein eL38 / 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 / Nucleolar GTP-binding protein 2 / Ribosomal protein uL30-like / Translation machinery-associated protein 16 / Protein LLP homolog / MKI67 FHA domain-interacting nucleolar phosphoprotein / GTP-binding protein 4 / Protein SDA1 homolog / Ribosome biogenesis protein NOP53 / Probable ribosome biogenesis protein RLP24 / mRNA turnover protein 4 homolog / Leydig cell tumor 10 kDa protein homolog / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, Y. / Gao, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32230051;31922036 China
CitationJournal: Cell Res / Year: 2023
Title: Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Authors: Yunyang Zhang / Xiaomeng Liang / Sha Luo / Yan Chen / Yu Li / Chengying Ma / Ningning Li / Ning Gao /
Abstract: Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo ...Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.
History
DepositionMar 9, 2023Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
u: Ribosomal L1 domain-containing protein 1
f: Protein SDA1 homolog
q: 60S ribosomal protein L10a
t: MKI67 FHA domain-interacting nucleolar phosphoprotein
3: 60S ribosomal protein L7-like 1
2: 28S rRNA
4: GTP-binding protein 4
5: 5S rRNA
6: Eukaryotic translation initiation factor 6
7: Probable ribosome biogenesis protein RLP24
9: Zinc finger protein 593
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
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
S: 60S ribosomal protein L14
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
g: 60S ribosomal protein L23a
h: 60S ribosomal protein L26
i: 60S ribosomal protein L27
j: 60S ribosomal protein L31
k: 60S ribosomal protein L32
l: 60S ribosomal protein L28
m: 60S ribosomal protein L8
n: 60S ribosomal protein L35a
o: 60S ribosomal protein L6
p: 60S ribosomal protein L7
r: 60S ribosomal protein L5
z: Protein LLP homolog
A: G Protein Nucleolar 2
R: Translation machinery-associated protein 16
J: mRNA turnover protein 4 homolog
T: Leydig cell tumor 10 kDa protein homolog
y: 60S ribosomal protein L12
v: Pescadillo homolog
8: 5.8S rRNA
1: Uncharacterized protein C11orf98
s: Ribosome biogenesis protein NSA2 homolog
w: Ribosome biogenesis protein NOP53
x: Internal Transcribed Spacer 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,223,07264
Polymers3,222,56561
Non-polymers5073
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 14 types, 14 molecules uft4679zARJTv1

#1: Protein Ribosomal L1 domain-containing protein 1 / CATX-11 / Cellular senescence-inhibited gene protein / Protein PBK1


Mass: 55089.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O76021
#2: Protein Protein SDA1 homolog / Nucleolar protein 130 / SDA1 domain-containing protein 1 / hSDA


Mass: 80005.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVU7
#4: Protein MKI67 FHA domain-interacting nucleolar phosphoprotein / Nucleolar phosphoprotein Nopp34 / Nucleolar protein interacting with the FHA domain of pKI-67 / hNIFK


Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYG3
#7: Protein GTP-binding protein 4 / Chronic renal failure gene protein / GTP-binding protein NGB


Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE4
#9: 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
#10: Protein Probable ribosome biogenesis protein RLP24 / Ribosomal L24 domain-containing protein 1 / Ribosomal protein L24-like


Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UHA3
#11: Protein Zinc finger protein 593 / Zinc finger protein T86


Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00488
#50: Protein Protein LLP homolog / Protein LAPS18-like


Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRT6
#51: Protein G Protein Nucleolar 2 / Autoantigen NGP-1


Mass: 83796.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13823
#52: Protein Translation machinery-associated protein 16


Mass: 23912.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY4
#53: Protein mRNA turnover protein 4 homolog / Ribosome assembly factor MRTO4


Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UKD2
#54: Protein Leydig cell tumor 10 kDa protein homolog


Mass: 10605.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNZ5
#56: Protein Pescadillo homolog


Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00541
#58: Protein Uncharacterized protein C11orf98


Mass: 14272.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: E9PRG8

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60S ribosomal protein ... , 41 types, 41 molecules q3BCDEFGHIKLMNOPQSUVWXYZabcdeg...

#3: 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
#5: Protein 60S ribosomal protein L7-like 1 / Large ribosomal subunit protein uL30-like 1


Mass: 29730.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6DKI1
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#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 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
#43: 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
#44: 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
#45: 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
#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
#49: 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
#55: Protein 60S ribosomal protein L12 / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050

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RNA chain , 4 types, 4 molecules 258x

#6: RNA chain 28S rRNA


Mass: 1636639.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: NR_146154.1 / Source: (natural) Homo sapiens (human)
#8: RNA chain 5S rRNA


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


Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: KY962518
#61: RNA chain Internal Transcribed Spacer 2


Mass: 23486.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence ID: X17626.1 / Source: (natural) Homo sapiens (human)

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Ribosome biogenesis protein ... , 2 types, 2 molecules sw

#59: Protein Ribosome biogenesis protein NSA2 homolog / Hairy cell leukemia protein 1 / TGF-beta-inducible nuclear protein 1


Mass: 30136.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95478
#60: Protein Ribosome biogenesis protein NOP53 / Glioma tumor suppressor candidate region gene 2 protein / Protein interacting with carboxyl ...Glioma tumor suppressor candidate region gene 2 protein / Protein interacting with carboxyl terminus 1 / PICT-1 / p60


Mass: 54498.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZM5

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Non-polymers , 3 types, 3 molecules

#62: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#63: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#64: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN
Has protein modificationN

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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: cryo-EM structure of human nuclear pre-60S ribosomal particle - State F'
Type: RIBOSOME / Entity ID: #1-#4, #61, #5-#60 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45905 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01181398
ELECTRON MICROSCOPYf_angle_d1.254263650
ELECTRON MICROSCOPYf_dihedral_angle_d16.16758770
ELECTRON MICROSCOPYf_chiral_restr0.06332216
ELECTRON MICROSCOPYf_plane_restr0.01118690

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