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- PDB-7r81: Structure of the translating Neurospora crassa ribosome arrested ... -

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Basic information

Entry
Database: PDB / ID: 7r81
TitleStructure of the translating Neurospora crassa ribosome arrested by cycloheximide
Components
  • (40S ribosomal protein ...) x 28
  • (60S ribosomal protein ...) x 34
  • (Ribosomal protein ...) x 6
  • 18S rRNA18S ribosomal RNA
  • 26S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60s ribosomal protein
  • Cytoplasmic ribosomal protein 10
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Nascent peptide
  • Probable 40s ribosomal protein s10-b
  • Ribosomal_L28e domain-containing protein
  • Ubiquitin-40S ribosomal protein S27a
  • hypothetical protein NCU16635 (eL41)Hypothesis
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsTRANSLATION / Protein Synthesis Inhibitor / Cytosolic Ribosome / Polysomal Ribosome / Peptidyl Transferase Center
Function / homology
Function and homology information


positive regulation of translational fidelity / : / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase A catalytic subunit binding / protein-RNA complex assembly / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / translational termination ...positive regulation of translational fidelity / : / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase A catalytic subunit binding / protein-RNA complex assembly / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / small-subunit processome / assembly of large subunit precursor of preribosome / protein kinase C binding / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal large subunit assembly / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / 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 protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein S7e / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal L27e protein family / Ribosomal protein S4, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal
Similarity search - Domain/homology
Chem-3HE / SPERMIDINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein ...Chem-3HE / SPERMIDINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / 60S ribosomal protein L35 / 40S ribosomal protein S7 / 60S ribosomal protein L5 / 40S ribosomal protein S21 / 60S ribosomal protein L28 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S26E / 40S ribosomal protein S17 / 60S ribosomal protein L3 / 40S ribosomal protein S0 / Guanine nucleotide-binding protein subunit beta-like protein / Ribosomal protein L26 / 60S ribosomal protein L27 / 40S ribosomal protein S24 / 60S ribosomal protein L22 / 60S ribosomal protein L4-A / 60S ribosomal protein L8 / Cytoplasmic ribosomal protein 10 / 40S ribosomal protein S12 / 40S ribosomal protein S22 / 40S ribosomal protein S5 / 60S ribosomal protein L44 / 60S ribosomal protein L11 / 40S ribosomal protein S27 / 60S ribosomal protein L2 / 60S ribosomal protein L34 / 60s ribosomal protein / 60S ribosomal protein L18 / 40S ribosomal protein S18 / 60S ribosomal protein L32 / 60S ribosomal protein L29 / 60S ribosomal protein L33 / 60S ribosomal protein L43 / 60S ribosomal protein L39 / 40S ribosomal protein S20 / 40S ribosomal protein S2 / Ribosomal protein L19 / 40S ribosomal protein S28 / 60S ribosomal protein L13 / 60S ribosomal protein L10 / 60S ribosomal protein L30 / Ribosomal_L28e domain-containing protein / 60S ribosomal protein L7 / 40S ribosomal protein S19 / 60S ribosomal protein L25 / 40S ribosomal protein S25 / 40S ribosomal protein S13 / 60S ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein Srp1 / 40S ribosomal protein S4 / 60S ribosomal protein L36 / 40S ribosomal protein S16 / 40S ribosomal protein S11 / 60S ribosomal protein L9 / Ribosomal protein S12 / 60S ribosomal protein L6 / 60S ribosomal protein L23 / Ribosomal protein L14 / 40S ribosomal protein S1 / Probable 40s ribosomal protein s10-b / 60S ribosomal protein L15 / 60S ribosomal protein L38 / 40S ribosomal protein S29 / 60S ribosomal protein L17 / 40S ribosomal protein S23 / 60S ribosomal protein L41 / 60S ribosomal protein L16 / 40S ribosomal protein S30 / 60S ribosomal protein L40 / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Ribosomal protein L37 / 60S ribosomal protein L20
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsShen, L. / Su, Z. / Yang, K. / Wu, C. / Becker, T. / Bell-Pedersen, D. / Zhang, J. / Sachs, M.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI138158 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126966 United States
Welch FoundationA1863 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure of the translating ribosome arrested by cycloheximide.
Authors: Lunda Shen / Zhaoming Su / Kailu Yang / Cheng Wu / Thomas Becker / Deborah Bell-Pedersen / Junjie Zhang / Matthew S Sachs /
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 ...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 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 , yeast, and humans all contain a highly conserved CHX binding site. We also sequenced classic 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 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.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A1: 26S rRNA
A2: 18S rRNA
B1: 5S rRNA
B2: 40S ribosomal protein S0
C1: 5.8S rRNA
C2: 40S ribosomal protein S1
D1: 60S ribosomal protein L2
D2: 40S ribosomal protein S2
E1: 60S ribosomal protein L3
E2: Cytoplasmic ribosomal protein 10
F1: 60S ribosomal protein L4-A
F2: 40S ribosomal protein S4
G1: 60S ribosomal protein L5
G2: 40S ribosomal protein S5
H1: 60S ribosomal protein L6
H2: 40S ribosomal protein S6
I1: 60S ribosomal protein L7
I2: 40S ribosomal protein S7
J1: 60S ribosomal protein L8
J2: 40S ribosomal protein S8
K1: 60S ribosomal protein L9
K2: 40S ribosomal protein S9
L1: 60S ribosomal protein L10
L2: Probable 40s ribosomal protein s10-b
M1: 60S ribosomal protein L11
M2: 40S ribosomal protein S11
N1: 60S ribosomal protein L13
N2: 40S ribosomal protein S12
O1: Ribosomal protein L14
O2: 40S ribosomal protein S13
P1: 60S ribosomal protein L15
P2: 40S ribosomal protein S14 (uS11)
Q1: 60S ribosomal protein L16
Q2: Ribosomal protein S12
R1: 60S ribosomal protein L17
R2: 40S ribosomal protein S16
S1: 60S ribosomal protein L18
S2: 40S ribosomal protein S17
T1: Ribosomal protein L19
T2: 40S ribosomal protein S18
U1: 60S ribosomal protein L20
U2: 40S ribosomal protein S19
V1: Ribosomal protein Srp1
V2: 40S ribosomal protein S20
W1: 60S ribosomal protein L22
W2: 40S ribosomal protein S21
X1: 60S ribosomal protein L23
X2: 40S ribosomal protein S22
Y1: 60S ribosomal protein L24
Y2: 40S ribosomal protein S23
Z1: 60S ribosomal protein L25
Z2: 40S ribosomal protein S24
a1: Ribosomal protein L26
a2: 40S ribosomal protein S25
b1: 60S ribosomal protein L27 (eL27)
b2: 40S ribosomal protein S26E
c1: 60S ribosomal protein L28
c2: 40S ribosomal protein S27
d1: 60S ribosomal protein L29
d2: 40S ribosomal protein S28
e1: 60S ribosomal protein L30
e2: 40S ribosomal protein S29
f1: 60s ribosomal protein
f2: 40S ribosomal protein S30
g1: 60S ribosomal protein L32
g2: Ubiquitin-40S ribosomal protein S27a
h1: 60S ribosomal protein L33
h2: Guanine nucleotide-binding protein subunit beta-like protein
i1: 60S ribosomal protein L34
j1: 60S ribosomal protein L35
k1: 60S ribosomal protein L36
l1: Ribosomal protein L37
m1: 60S ribosomal protein L38
n1: 60S ribosomal protein L39
o1: 60S ribosomal protein L40
p1: hypothetical protein NCU16635 (eL41)
q1: 60S ribosomal protein L44
r1: 60S ribosomal protein L43
s1: Ribosomal_L28e domain-containing protein
t1: tRNA
u1: tRNA
v1: Nascent peptide
w1: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,192,293345
Polymers3,185,54783
Non-polymers6,746262
Water0
1


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

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Components

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RNA chain , 6 types, 7 molecules A1A2B1C1t1u1w1

#1: RNA chain 26S rRNA


Mass: 1078431.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: GenBank: 209980056
#2: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 578821.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: GenBank: 209980056
#3: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38579.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: GenBank: 168880
#5: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50770.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: GenBank: 168899
#80: RNA chain tRNA / Transfer RNA


Mass: 24468.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: One molecule is found in the A-site, and one molecule is found in the P-site. No specific tRNAs are represented in the peptidyltransferase centers of polysomal ribosomes. Therefore, we ...Details: One molecule is found in the A-site, and one molecule is found in the P-site. No specific tRNAs are represented in the peptidyltransferase centers of polysomal ribosomes. Therefore, we adapted the tRNA model for a eukaryotic ICG-anticodon tRNA that decodes Arg codons (PDB ID: 6T4Q) to model the tRNA densities of both A- and P-site tRNAs.
Source: (natural) Neurospora crassa (fungus)
#82: RNA chain mRNA / Messenger RNA


Mass: 5159.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: No specific mRNA is represented in the polysomal ribosomes. Therefore, we used Uracil to model the mRNA.
Source: (natural) Neurospora crassa (fungus)

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40S ribosomal protein ... , 28 types, 28 molecules B2C2D2F2G2H2I2J2K2M2N2O2P2R2S2T2U2V2W2X2Y2Z2a2b2c2d2e2f2

#4: Protein 40S ribosomal protein S0 / / Ribosome-associated protein 1


Mass: 31529.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q01291
#6: Protein 40S ribosomal protein S1 / / Cytoplasmic ribosomal protein 8


Mass: 29123.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q871N9
#8: Protein 40S ribosomal protein S2 /


Mass: 28807.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S503
#12: Protein 40S ribosomal protein S4 /


Mass: 29654.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SE03
#14: Protein 40S ribosomal protein S5 /


Mass: 23715.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVI1
#16: Protein 40S ribosomal protein S6 /


Mass: 27395.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5INQ2
#18: Protein 40S ribosomal protein S7 / / Cytoplasmic ribosomal protein 15


Mass: 22913.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: O43105
#20: Protein 40S ribosomal protein S8 /


Mass: 23061.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5IPM8
#22: Protein 40S ribosomal protein S9 /


Mass: 21852.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SDY7
#26: Protein 40S ribosomal protein S11 /


Mass: 18468.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SFZ2
#28: Protein 40S ribosomal protein S12 /


Mass: 16250.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RV74
#30: Protein 40S ribosomal protein S13 /


Mass: 16904.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SDH0
#32: Protein 40S ribosomal protein S14 (uS11) / Ribosome


Mass: 16025.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DYT5
#36: Protein 40S ribosomal protein S16 /


Mass: 15752.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SFJ9
#38: Protein 40S ribosomal protein S17 / / CRP3


Mass: 16974.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: P27770
#40: Protein 40S ribosomal protein S18 /


Mass: 17806.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RXX0
#42: Protein 40S ribosomal protein S19 /


Mass: 16700.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SBD8
#44: Protein 40S ribosomal protein S20 /


Mass: 13250.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S3G1
#46: Protein 40S ribosomal protein S21 / / Cytoplasmic ribosomal protein 7


Mass: 9674.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: O93798
#48: Protein 40S ribosomal protein S22 / / Cytoplasmic ribosomal protein 27


Mass: 14846.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RV75
#50: Protein 40S ribosomal protein S23 / / Cytoplasmic ribosomal protein 28


Mass: 15944.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9HE74
#52: Protein 40S ribosomal protein S24 /


Mass: 15598.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q1K5V9
#54: Protein 40S ribosomal protein S25 /


Mass: 10822.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SC06
#56: Protein 40S ribosomal protein S26E / Ribosome / 13.6 kDa ribosomal protein / CRP5


Mass: 13580.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: P21772
#58: Protein 40S ribosomal protein S27 / / Cytoplasmic ribosomal protein 6


Mass: 8910.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVN2
#60: Protein 40S ribosomal protein S28 /


Mass: 7735.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S6W5
#62: Protein 40S ribosomal protein S29 /


Mass: 6515.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9C2P2
#64: Protein 40S ribosomal protein S30 /


Mass: 6912.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5IMG5

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60S ribosomal protein ... , 34 types, 34 molecules D1E1F1G1H1I1J1K1L1M1N1P1Q1R1S1U1W1X1Y1Z1b1c1d1e1g1h1i1j1k1m1...

#7: Protein 60S ribosomal protein L2 /


Mass: 27410.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVQ9
#9: Protein 60S ribosomal protein L3 /


Mass: 44131.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: P59671
#11: Protein 60S ribosomal protein L4-A / Ribosome


Mass: 38882.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q1K7B7
#13: Protein 60S ribosomal protein L5 / / CPR4


Mass: 34470.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: O59953
#15: Protein 60S ribosomal protein L6 /


Mass: 22516.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SH22
#17: Protein 60S ribosomal protein L7 /


Mass: 28741.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SBD5
#19: Protein 60S ribosomal protein L8 /


Mass: 29427.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q6MFL6
#21: Protein 60S ribosomal protein L9 /


Mass: 21787.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SGA6
#23: Protein 60S ribosomal protein L10 /


Mass: 25373.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S7F0
#25: Protein 60S ribosomal protein L11 /


Mass: 20123.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVN0
#27: Protein 60S ribosomal protein L13 /


Mass: 23929.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S709
#31: Protein 60S ribosomal protein L15 /


Mass: 24250.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X034
#33: Protein 60S ribosomal protein L16 /


Mass: 26184.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5ILK7
#35: Protein 60S ribosomal protein L17 /


Mass: 20802.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9HE25
#37: Protein 60S ribosomal protein L18 /


Mass: 20651.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RXJ4
#41: Protein 60S ribosomal protein L20 /


Mass: 20385.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5IQT8
#45: Protein 60S ribosomal protein L22 /


Mass: 14234.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q1K6Z3
#47: Protein 60S ribosomal protein L23 /


Mass: 14722.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SHJ9
#49: Protein 60S ribosomal protein L24 /


Mass: 17656.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SDU2
#51: Protein 60S ribosomal protein L25 /


Mass: 17158.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SBS9
#55: Protein 60S ribosomal protein L27 (eL27) / Ribosome


Mass: 15756.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q1K580
#57: Protein 60S ribosomal protein L28 / / CRP1 / L27A / L29


Mass: 16636.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: P08978
#59: Protein 60S ribosomal protein L29 /


Mass: 7488.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RZP9
#61: Protein 60S ribosomal protein L30 /


Mass: 11720.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S7F1
#65: Protein 60S ribosomal protein L32 / / Cytoplasmic ribosomal protein-63


Mass: 15001.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RXY1
#67: Protein 60S ribosomal protein L33 /


Mass: 12203.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S156
#69: Protein 60S ribosomal protein L34 /


Mass: 13225.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVY8
#70: Protein 60S ribosomal protein L35 /


Mass: 14445.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A7UW39
#71: Protein 60S ribosomal protein L36 /


Mass: 11587.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SEP1
#73: Protein 60S ribosomal protein L38 /


Mass: 9169.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9C2B9
#74: Protein 60S ribosomal protein L39 /


Mass: 6283.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S2X9
#75: Protein 60S ribosomal protein L40 / / 60S ribosomal protein L40 / variant


Mass: 6092.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5INI1
#77: Protein 60S ribosomal protein L44 /


Mass: 11945.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RVK8
#78: Protein 60S ribosomal protein L43 /


Mass: 10154.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S1Z1

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Protein , 6 types, 6 molecules E2L2f1g2h2s1

#10: Protein Cytoplasmic ribosomal protein 10 / 40S ribosomal protein S3 (uS3)


Mass: 28706.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RV52
#24: Protein Probable 40s ribosomal protein s10-b


Mass: 18463.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q873A6
#63: Protein 60s ribosomal protein /


Mass: 14097.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RW15
#66: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 17775.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: P14799
#68: Protein Guanine nucleotide-binding protein subunit beta-like protein / Cross-pathway control WD-repeat protein cpc-2


Mass: 35173.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q01369
#79: Protein Ribosomal_L28e domain-containing protein


Mass: 16011.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SBB3

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Ribosomal protein ... , 6 types, 6 molecules O1Q2T1V1a1l1

#29: Protein Ribosomal protein L14 /


Mass: 15885.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SI18
#34: Protein Ribosomal protein S12 /


Mass: 17419.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SGF1
#39: Protein Ribosomal protein L19 /


Mass: 22407.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S5N9
#43: Protein Ribosomal protein Srp1 /


Mass: 18253.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SDY8
#53: Protein Ribosomal protein L26 /


Mass: 15366.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q1K4V7
#72: Protein Ribosomal protein L37 /


Mass: 10261.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5IQ48

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Protein/peptide , 2 types, 2 molecules p1v1

#76: Protein/peptide hypothetical protein NCU16635 (eL41) / Hypothesis


Mass: 3384.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: U9WGG3
#81: Protein/peptide Nascent peptide


Mass: 358.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: No specific nascent peptide is represented in the polysomal ribosomes. Therefore, we used UNK (unknown residue) to represent each residue of the nascent peptide.
Source: (natural) Neurospora crassa (fungus)

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Non-polymers , 3 types, 262 molecules

#83: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione / Cycloheximide


Mass: 281.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#84: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#85: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 260 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of the translating Neurospora crassa ribosome arrested by cycloheximideRIBOSOME#1-#820NATURAL
260S ribosomal subunitRIBOSOME#1, #3, #5, #7, #9, #11, #13, #15, #17, #19, #21, #23, #25, #27, #29, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #53, #55, #57, #59, #61, #63, #65, #67, #69-#791NATURAL
340S ribosomal subunitRIBOSOME#2, #4, #6, #8, #10, #12, #14, #16, #18, #20, #22, #24, #26, #28, #30, #32, #34, #36, #38, #40, #42, #44, #46, #48, #50, #52, #54, #56, #58, #60, #62, #64, #66, #681NATURAL
4tRNATransfer RNACOMPLEX#801NATURAL
5Nascent peptideCOMPLEX#811NATURAL
6mRNAMessenger RNACOMPLEX#821NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Neurospora crassa (fungus)5141
33Neurospora crassa (fungus)5141
44Neurospora crassa (fungus)5141
55Neurospora crassa (fungus)5141
66Neurospora crassa (fungus)5141
Buffer solutionpH: 7.6
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
Image recordingElectron dose: 32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196154 / Symmetry type: POINT

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