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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 rRNA
  • 26S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 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)
  • mRNA
  • tRNA
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 / protein kinase A catalytic subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity ...: / positive regulation of translational fidelity / preribosome, small subunit precursor / protein kinase A catalytic subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / large ribosomal subunit / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, 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
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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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
Water00
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


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


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


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


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


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)


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 / 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


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)


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)


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


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)


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
4tRNACOMPLEX#801NATURAL
5Nascent peptideCOMPLEX#811NATURAL
6mRNACOMPLEX#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 FIELD
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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