7R81

Structure of the translating Neurospora crassa ribosome arrested by cycloheximide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the translating Neurospora ribosome arrested by cycloheximide

Shen, L.Su, Z.Yang, K.Wu, C.Becker, T.Bell-Pedersen, D.Zhang, J.Sachs, M.S.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2111862118
  • Primary Citation of Related Structures:  
    7R81

  • PubMed Abstract: 
  • Ribosomes translate RNA into proteins. The protein synthesis inhibitor cycloheximide (CHX) is widely used to inhibit eukaryotic ribosomes engaged in translation elongation. However, the lack of structural data for actively translating polyribosomes stalled by CHX leaves unanswered the question of which elongation step is inhibited ...

    Ribosomes translate RNA into proteins. The protein synthesis inhibitor cycloheximide (CHX) is widely used to inhibit eukaryotic ribosomes engaged in translation elongation. However, the lack of structural data for actively translating polyribosomes stalled by CHX leaves unanswered the question of which elongation step is inhibited. We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution. The ribosome structure from this filamentous fungus contains clearly resolved ribosomal protein eL28, like higher eukaryotes but unlike budding yeast, which lacks eL28. Despite some differences in overall structures, the ribosomes from Neurospora , yeast, and humans all contain a highly conserved CHX binding site. We also sequenced classic Neurospora CHX-resistant alleles. These mutations, including one at a residue not previously observed to affect CHX resistance in eukaryotes, were in the large subunit proteins uL15 and eL42 that are part of the CHX-binding pocket. In addition to A-site transfer RNA (tRNA), P-site tRNA, messenger RNA, and CHX that are associated with the translating N. crassa ribosome, spermidine is present near the CHX binding site close to the E site on the large subunit. The tRNAs in the peptidyl transferase center are in the A/A site and the P/P site. The nascent peptide is attached to the A-site tRNA and not to the P-site tRNA. The structural and functional data obtained show that CHX arrests the ribosome in the classical PRE translocation state and does not interfere with A-site reactivity.


    Organizational Affiliation

    Department of Biology, Texas A&M University, College Station, TX 77843; msachs@bio.tamu.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0D [auth B2]290Neurospora crassaMutation(s): 0 
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Find proteins for Q01291 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1F [auth C2]256Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q871N9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2G [auth D1]254Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7RVQ9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2H [auth D2]265Neurospora crassaMutation(s): 0 
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Find proteins for Q7S503 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3I [auth E1]392Neurospora crassaMutation(s): 0 
UniProt
Find proteins for P59671 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytoplasmic ribosomal protein 10J [auth E2]262Neurospora crassaMutation(s): 0 
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Find proteins for Q7RV52 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AK [auth F1]361Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q1K7B7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4L [auth F2]261Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7SE03 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 13
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60S ribosomal protein L5M [auth G1]301Neurospora crassaMutation(s): 0 
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Find proteins for O59953 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5N [auth G2]213Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7RVI1 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6O [auth H1]202Neurospora crassaMutation(s): 0 
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Find proteins for Q7SH22 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6P [auth H2]239Neurospora crassaMutation(s): 0 
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Find proteins for V5INQ2 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7Q [auth I1]248Neurospora crassaMutation(s): 0 
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Find proteins for Q7SBD5 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7R [auth I2]202Neurospora crassaMutation(s): 0 
UniProt
Find proteins for O43105 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8S [auth J1]262Neurospora crassaMutation(s): 0 
Gene Names: B15B10.040
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Find proteins for Q6MFL6 (Neurospora crassa)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8T [auth J2]202Neurospora crassaMutation(s): 0 
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Find proteins for V5IPM8 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9U [auth K1]193Neurospora crassaMutation(s): 0 
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Find proteins for Q7SGA6 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9V [auth K2]190Neurospora crassaMutation(s): 0 
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Find proteins for Q7SDY7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10W [auth L1]221Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7S7F0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 40s ribosomal protein s10-bX [auth L2]163Neurospora crassaMutation(s): 0 
Gene Names: B24N11.180GE21DRAFT_3150
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Find proteins for Q873A6 (Neurospora crassa)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11Y [auth M1]174Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7RVN0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11Z [auth M2]161Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7SFZ2 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13AA [auth N1]214Neurospora crassaMutation(s): 0 
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Find proteins for Q7S709 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12BA [auth N2]147Neurospora crassaMutation(s): 0 
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Find proteins for Q7RV74 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 29
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Ribosomal protein L14CA [auth O1]142Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7SI18 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 30
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40S ribosomal protein S13DA [auth O2]151Neurospora crassaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15EA [auth P1]203Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q8X034 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14 (uS11)FA [auth P2]150Neurospora crassaMutation(s): 0 
Gene Names: GE21DRAFT_3956
UniProt
Find proteins for A0A0B0DYT5 (Neurospora crassa)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16GA [auth Q1]231Neurospora crassaMutation(s): 0 
UniProt
Find proteins for V5ILK7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 34
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Ribosomal protein S12HA [auth Q2]152Neurospora crassaMutation(s): 0 
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Find proteins for Q7SGF1 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17IA [auth R1]186Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q9HE25 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16JA [auth R2]142Neurospora crassaMutation(s): 0 
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Find proteins for Q7SFJ9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 37
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60S ribosomal protein L18KA [auth S1]183Neurospora crassaMutation(s): 0 
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Find proteins for Q7RXJ4 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 38
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40S ribosomal protein S17LA [auth S2]146Neurospora crassaMutation(s): 0 
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Find proteins for P27770 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 39
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Ribosomal protein L19MA [auth T1]192Neurospora crassaMutation(s): 0 
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Find proteins for Q7S5N9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 40
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40S ribosomal protein S18NA [auth T2]156Neurospora crassaMutation(s): 0 
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Find proteins for Q7RXX0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 41
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60S ribosomal protein L20OA [auth U1]174Neurospora crassaMutation(s): 0 
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Find proteins for V5IQT8 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 42
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40S ribosomal protein S19PA [auth U2]149Neurospora crassaMutation(s): 0 
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Find proteins for Q7SBD8 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 43
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Ribosomal protein Srp1QA [auth V1]160Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20RA [auth V2]117Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22SA [auth W1]126Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21TA [auth W2]87Neurospora crassaMutation(s): 0 
UniProt
Find proteins for O93798 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 47
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60S ribosomal protein L23UA [auth X1]139Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22VA [auth X2]130Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7RV75 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24WA [auth Y1]156Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23XA [auth Y2]145Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25YA [auth Z1]156Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24ZA [auth Z2]136Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L26AB [auth a1]136Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25BB [auth a2]97Neurospora crassaMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27 (eL27)CB [auth b1]135Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26EDB [auth b2]119Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28EB [auth c1]149Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27FB [auth c2]82Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 59
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60S ribosomal protein L29GB [auth d1]65Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28HB [auth d2]68Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30IB [auth e1]109Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 62
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40S ribosomal protein S29JB [auth e2]56Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60s ribosomal proteinKB [auth f1]122Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 64
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40S ribosomal protein S30LB [auth f2]63Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 65
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60S ribosomal protein L32MB [auth g1]131Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 66
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Ubiquitin-40S ribosomal protein S27aNB [auth g2]154Neurospora crassaMutation(s): 0 
UniProt
Find proteins for P14799 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33OB [auth h1]109Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinPB [auth h2]316Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q01369 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34QB [auth i1]117Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35RB [auth j1]125Neurospora crassaMutation(s): 0 
UniProt
Find proteins for A7UW39 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36SB [auth k1]104Neurospora crassaMutation(s): 0 
UniProt
Find proteins for Q7SEP1 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37TB [auth l1]92Neurospora crassaMutation(s): 0 
UniProt
Find proteins for V5IQ48 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth m1]80Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39VB [auth n1]51Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L40WB [auth o1]52Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical protein NCU16635 (eL41)XB [auth p1]25Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L44YB [auth q1]106Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43ZB [auth r1]92Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L28e domain-containing proteinAC [auth s1]150Neurospora crassaMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
Nascent peptideDC [auth v1]4Neurospora crassaMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
26S rRNAA [auth A1]3,338Neurospora crassa
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Entity ID: 2
MoleculeChainsLengthOrganismImage
18S rRNAB [auth A2]1,796Neurospora crassa
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S rRNAC [auth B1]120Neurospora crassa
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5.8S rRNAE [auth C1]158Neurospora crassa
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Entity ID: 80
MoleculeChainsLengthOrganismImage
tRNABC [auth t1],
CC [auth u1]
76Neurospora crassa
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Entity ID: 82
MoleculeChainsLengthOrganismImage
mRNAEC [auth w1]17Neurospora crassa
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HE (Subject of Investigation/LOI)
Query on 3HE

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FC [auth A1]4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
 Ligand Interaction
SPD
Query on SPD

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GC [auth A1]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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