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- PDB-29ix: Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2... -

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Basic information

Entry
Database: PDB / ID: 29ix
TitleHuman monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified ribosomes as control.
Components
  • (60S ribosomal protein ...) x 32
  • (Large ribosomal subunit protein ...) x 8
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Ribosomal protein uL16-like
KeywordsRIBOSOME / Toxin NT-2 / translation inhibitor / mycotoxin / trichothecene
Function / homology
Function and homology information


male meiosis I / translation at presynapse / response to insecticide / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / G1 to G0 transition / negative regulation of formation of translation preinitiation complex / GAIT complex / TORC2 complex binding ...male meiosis I / translation at presynapse / response to insecticide / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / G1 to G0 transition / negative regulation of formation of translation preinitiation complex / GAIT complex / TORC2 complex binding / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of translation involved in cellular response to UV / A band / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to aldosterone / negative regulation of myoblast fusion / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / Protein hydroxylation / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / protein localization to nucleus / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein targeting / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / embryo implantation / L13a-mediated translational silencing of Ceruloplasmin expression / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / MDM2/MDM4 family protein binding / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Activation of STAT3 by cadherin engagement / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of signal transduction by p53 class mediator / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / PD-L1(CD274) glycosylation and translocation to plasma membrane / protein modification process / NRIF signals cell death from the nucleus / Downregulation of ERBB2:ERBB3 signaling / Regulation of PTEN localization / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / ribosomal large subunit biogenesis / Translesion synthesis by POLK / Regulation of BACH1 activity / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Downregulation of TGF-beta receptor signaling
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein L19, eukaryotic / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L10e / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal L18 C-terminal region / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal L40e family / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein L6e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L31e, conserved site / : / Ribosomal protein L31e signature. / Ribosomal protein L18e / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L35A
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / SPERMINE / : / : / RNA / RNA (> 10) ...: / ADENOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / SPERMINE / : / : / 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 / 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 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 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsRabl, J. / Karousis, E.D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSK-3_220624 Switzerland
CitationJournal: To Be Published
Title: Toxin NT-2 bound to human ribosome
Authors: Rabl, J. / Karousis, E.D.
History
DepositionMar 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Large ribosomal subunit protein uL30
AB: 60S ribosomal protein L7a
AC: 60S ribosomal protein L9
AD: Ribosomal protein uL16-like
AE: 60S ribosomal protein L11
AF: 60S ribosomal protein L13
AG: 60S ribosomal protein L14
AH: 60S ribosomal protein L15
AI: 60S ribosomal protein L13a
AJ: 60S ribosomal protein L17
AK: 60S ribosomal protein L18
AL: 60S ribosomal protein L19
AM: 60S ribosomal protein L18a
AN: 60S ribosomal protein L21
AO: 60S ribosomal protein L22
AP: 60S ribosomal protein L23
AQ: 60S ribosomal protein L24
AR: 60S ribosomal protein L23a
AS: 60S ribosomal protein L26
AT: 60S ribosomal protein L27
AU: Large ribosomal subunit protein uL15
AV: 60S ribosomal protein L29
AW: 60S ribosomal protein L30
AX: 60S ribosomal protein L31
AY: 60S ribosomal protein L32
AZ: Large ribosomal subunit protein eL33
Aa: 60S ribosomal protein L34
Ab: 60S ribosomal protein L35
Ac: 60S ribosomal protein L36
Ad: Large ribosomal subunit protein eL37
Ae: 60S ribosomal protein L38
Af: 60S ribosomal protein L39
Ag: Large ribosomal subunit protein eL40
Ah: 60S ribosomal protein L36a
Ai: 60S ribosomal protein L37a
Aj: 60S ribosomal protein L28
BA: Large ribosomal subunit protein uL3
BB: 60S ribosomal protein L4
BC: 60S ribosomal protein L5
BD: Large ribosomal subunit protein eL6
DA: 28S rRNA
DB: 5S rRNA
DC: 5.8S rRNA
DD: Large ribosomal subunit protein uL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,564,252292
Polymers2,555,10344
Non-polymers9,149248
Water182,74410144
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  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 8 types, 8 molecules AAAUAZAdAgBABDDD

#1: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#21: Protein Large ribosomal subunit protein uL15


Mass: 16619.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#26: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#30: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#33: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40


Mass: 14771.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#37: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B


Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#40: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#44: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917

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60S ribosomal protein ... , 32 types, 32 molecules ABACAEAFAGAHAIAJAKALAMANAOAPAQARASATAVAWAXAYAaAbAcAeAfAhAiAjBBBC

#2: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#3: 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
#5: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / 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
#6: Protein 60S ribosomal protein L13 / Breast basic conserved protein 1 / 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
#7: Protein 60S ribosomal protein L14 / CAG-ISL 7 / 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
#8: 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
#9: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / 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
#10: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#11: 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
#12: 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
#13: 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
#14: 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
#15: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / 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
#16: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / 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
#17: Protein 60S ribosomal protein L24 / 60S ribosomal protein L30 / 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
#18: 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
#19: 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
#20: 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
#22: Protein 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / 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
#23: 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
#24: 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
#25: 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
#27: 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
#28: 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
#29: 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
#31: 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
#32: 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
#34: Protein 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / 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
#35: 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
#36: 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
#38: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / 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
#39: 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

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Protein , 1 types, 1 molecules AD

#4: Protein Ribosomal protein uL16-like / 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

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RNA chain , 3 types, 3 molecules DADBDC

#41: RNA chain 28S rRNA


Mass: 1640816.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#42: 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: 23898
#43: RNA chain 5.8S rRNA


Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853

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Non-polymers , 9 types, 10392 molecules

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


Mass: 24.305 Da / Num. of mol.: 184 / Source method: obtained synthetically / Formula: Mg
#46: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: K
#47: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#48: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12N2
#49: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3
#50: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#51: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#52: Chemical ChemComp-A1JQ4 / Toxin NT-2 / [(1~{S},2~{R},4~{S},7~{R},9~{R},10~{R},11~{S},12~{S})-2-(hydroxymethyl)-1,5-dimethyl-4,10-bis(oxidanyl)spiro[8-oxatricyclo[7.2.1.0^{2,7}]dodec-5-ene-12,2'-oxirane]-11-yl] ethanoate


Mass: 340.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24O7 / Feature type: SUBJECT OF INVESTIGATION
#53: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Human 60S ribosomal subunit / Type: RIBOSOME
Details: Human 60S ribosomal subunit incubated with toxin NT-2
Entity ID: #1-#44 / 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-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 616107 / Symmetry type: POINT

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