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- PDB-8pnn: 80S yeast ribosome in complex with Bromolissoclimide -

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Basic information

Entry
Database: PDB / ID: 8pnn
Title80S yeast ribosome in complex with Bromolissoclimide
Components
  • (40S ribosomal protein ...) x 26
  • (60S ribosomal protein ...) x 38
  • (Large ribosomal subunit protein ...) x 3
  • (Small ribosomal subunit protein ...) x 4
  • 16S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Suppressor protein STM1
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Ribosome inhibition / eL42
Function / homology
Function and homology information


triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / TOR signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / maturation of LSU-rRNA / 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) / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / telomere maintenance / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / 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) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding
Similarity search - Function
Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L6e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S3Ae, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae signature. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Ribosomal protein S3, eukaryotic/archaeal
Similarity search - Domain/homology
: / osmium (III) hexammine / SPERMIDINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...: / osmium (III) hexammine / SPERMIDINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Suppressor protein STM1 / Small ribosomal subunit protein uS11B / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTerrosu, S. / Yusupov, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129264 United States
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Synthesis of Differentially Halogenated Lissoclimide Analogues To Probe Ribosome E-Site Binding.
Authors: Terrosu, S. / Nurullina, L. / Supantanapong, N. / Pak, B.S. / Nguyen, S. / Holm, M. / Wu, C. / Lin, M. / Horne, D. / Sachs, M.S. / Blanchard, S.C. / Yusupov, M. / Vanderwal, C.D.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: 5S ribosomal RNA
AB: 60S ribosomal protein L28
CJ: 60S ribosomal protein L8-A
DJ: 60S ribosomal protein L35-A
Q: 40S ribosomal protein S15
s6: 40S ribosomal protein S6-A
4: 5.8S ribosomal RNA
AC: 60S ribosomal protein L29
CK: 60S ribosomal protein L9-A
DK: 60S ribosomal protein L36-A
R: 40S ribosomal protein S16-A
s7: 40S ribosomal protein S7-A
j: 60S ribosomal protein L2-A
AD: 60S ribosomal protein L30
CL: 60S ribosomal protein L10
DL: 60S ribosomal protein L37-A
S: 40S ribosomal protein S17-A
s8: 40S ribosomal protein S8-A
k: 60S ribosomal protein L3
AE: 60S ribosomal protein L31-A
CM: Large ribosomal subunit protein uL5B
DM: 60S ribosomal protein L38
T: 40S ribosomal protein S18-A
s9: 40S ribosomal protein S9-A
l: 60S ribosomal protein L4-A
AF: 60S ribosomal protein L32
CN: 60S ribosomal protein L13-A
DN: 60S ribosomal protein L39
U: 40S ribosomal protein S19-A
c0: 40S ribosomal protein S10-A
m: 60S ribosomal protein L5
AG: 60S ribosomal protein L33-A
CO: 60S ribosomal protein L14-A
DO: Ubiquitin-60S ribosomal protein L40
V: Small ribosomal subunit protein uS10
c1: 40S ribosomal protein S11-A
n: 60S ribosomal protein L6-A
AH: 60S ribosomal protein L34-A
CP: 60S ribosomal protein L15-A
DP: Large ribosomal subunit protein eL41B
W: 40S ribosomal protein S21-A
c3: 40S ribosomal protein S13
o: 60S ribosomal protein L7-A
AI: 60S ribosomal protein L35-A
CQ: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L42-A
X: 40S ribosomal protein S22-A
c4: 40S ribosomal protein S14-B
p: 60S ribosomal protein L8-A
AJ: 60S ribosomal protein L36-A
CR: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L43-A
Y: 40S ribosomal protein S23-A
c5: 40S ribosomal protein S15
q: 60S ribosomal protein L9-A
AK: 60S ribosomal protein L37-A
CS: 60S ribosomal protein L18-A
p0: Large ribosomal subunit protein uL10
Z: 40S ribosomal protein S24-A
c6: 40S ribosomal protein S16-A
r: 60S ribosomal protein L10
AL: 60S ribosomal protein L38
CT: 60S ribosomal protein L19-A
sM: Suppressor protein STM1
a: 40S ribosomal protein S25-A
c7: 40S ribosomal protein S17-A
s: Large ribosomal subunit protein uL5B
AM: 60S ribosomal protein L39
CU: 60S ribosomal protein L20-A
A: 16S ribosomal RNA
b: Small ribosomal subunit protein eS26B
c8: 40S ribosomal protein S18-A
t: 60S ribosomal protein L13-A
AN: Ubiquitin-60S ribosomal protein L40
CV: 60S ribosomal protein L21-A
B: 40S ribosomal protein S0-A
c: 40S ribosomal protein S27-A
c9: 40S ribosomal protein S19-A
u: 60S ribosomal protein L14-A
AO: Large ribosomal subunit protein eL41B
CW: 60S ribosomal protein L22-A
C: 40S ribosomal protein S1-A
d: 40S ribosomal protein S28-A
d0: Small ribosomal subunit protein uS10
w: 60S ribosomal protein L16-A
AP: 60S ribosomal protein L42-A
CX: 60S ribosomal protein L23-A
D: 40S ribosomal protein S2
e: Small ribosomal subunit protein uS14A
d1: 40S ribosomal protein S21-A
x: 60S ribosomal protein L17-A
AQ: 60S ribosomal protein L43-A
CY: 60S ribosomal protein L24-A
E: Small ribosomal subunit protein uS3
f: 40S ribosomal protein S30-A
d2: 40S ribosomal protein S22-A
y: 60S ribosomal protein L18-A
i: Suppressor protein STM1
CZ: 60S ribosomal protein L25
F: 40S ribosomal protein S4-A
g: Ubiquitin
d3: 40S ribosomal protein S23-A
z: 60S ribosomal protein L19-A
AR: 25S ribosomal RNA
DA: 60S ribosomal protein L26-A
G: 40S ribosomal protein S5
h: Guanine nucleotide-binding protein subunit beta-like protein
d4: 40S ribosomal protein S24-A
0: 60S ribosomal protein L20-A
AS: 5S ribosomal RNA
DB: 60S ribosomal protein L27-A
H: 40S ribosomal protein S6-A
sR: 16S ribosomal RNA
d5: 40S ribosomal protein S25-A
2: 60S ribosomal protein L21-A
AT: 5.8S ribosomal RNA
DC: 60S ribosomal protein L28
I: 40S ribosomal protein S7-A
Rb: Guanine nucleotide-binding protein subunit beta-like protein
d6: Small ribosomal subunit protein eS26B
5: 60S ribosomal protein L22-A
CD: 60S ribosomal protein L2-A
DD: 60S ribosomal protein L29
J: 40S ribosomal protein S8-A
s0: 40S ribosomal protein S0-A
d7: 40S ribosomal protein S27-A
6: 60S ribosomal protein L23-A
CE: 60S ribosomal protein L3
DE: 60S ribosomal protein L30
K: 40S ribosomal protein S9-A
s1: 40S ribosomal protein S1-A
d8: 40S ribosomal protein S28-A
7: 60S ribosomal protein L24-A
CF: 60S ribosomal protein L4-A
DF: 60S ribosomal protein L31-A
L: 40S ribosomal protein S10-A
s2: 40S ribosomal protein S2
d9: Small ribosomal subunit protein uS14A
8: 60S ribosomal protein L25
CG: 60S ribosomal protein L5
DG: 60S ribosomal protein L32
M: 40S ribosomal protein S11-A
s3: Small ribosomal subunit protein uS3
e0: 40S ribosomal protein S30-A
9: 60S ribosomal protein L26-A
CH: 60S ribosomal protein L6-A
DH: 60S ribosomal protein L33-A
O: 40S ribosomal protein S13
s4: 40S ribosomal protein S4-A
v: 60S ribosomal protein L15-A
AA: 60S ribosomal protein L27-A
CI: 60S ribosomal protein L7-A
DI: 60S ribosomal protein L34-A
P: 40S ribosomal protein S14-B
s5: 40S ribosomal protein S5
1: 25S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,564,0382606
Polymers6,257,497156
Non-polymers306,5412450
Water7,422412
1
3: 5S ribosomal RNA
AB: 60S ribosomal protein L28
Q: 40S ribosomal protein S15
4: 5.8S ribosomal RNA
AC: 60S ribosomal protein L29
R: 40S ribosomal protein S16-A
j: 60S ribosomal protein L2-A
AD: 60S ribosomal protein L30
S: 40S ribosomal protein S17-A
k: 60S ribosomal protein L3
AE: 60S ribosomal protein L31-A
T: 40S ribosomal protein S18-A
l: 60S ribosomal protein L4-A
AF: 60S ribosomal protein L32
U: 40S ribosomal protein S19-A
m: 60S ribosomal protein L5
AG: 60S ribosomal protein L33-A
V: Small ribosomal subunit protein uS10
n: 60S ribosomal protein L6-A
AH: 60S ribosomal protein L34-A
W: 40S ribosomal protein S21-A
o: 60S ribosomal protein L7-A
AI: 60S ribosomal protein L35-A
X: 40S ribosomal protein S22-A
p: 60S ribosomal protein L8-A
AJ: 60S ribosomal protein L36-A
Y: 40S ribosomal protein S23-A
q: 60S ribosomal protein L9-A
AK: 60S ribosomal protein L37-A
Z: 40S ribosomal protein S24-A
r: 60S ribosomal protein L10
AL: 60S ribosomal protein L38
a: 40S ribosomal protein S25-A
s: Large ribosomal subunit protein uL5B
AM: 60S ribosomal protein L39
A: 16S ribosomal RNA
b: Small ribosomal subunit protein eS26B
t: 60S ribosomal protein L13-A
AN: Ubiquitin-60S ribosomal protein L40
B: 40S ribosomal protein S0-A
c: 40S ribosomal protein S27-A
u: 60S ribosomal protein L14-A
AO: Large ribosomal subunit protein eL41B
C: 40S ribosomal protein S1-A
d: 40S ribosomal protein S28-A
w: 60S ribosomal protein L16-A
AP: 60S ribosomal protein L42-A
D: 40S ribosomal protein S2
e: Small ribosomal subunit protein uS14A
x: 60S ribosomal protein L17-A
AQ: 60S ribosomal protein L43-A
E: Small ribosomal subunit protein uS3
f: 40S ribosomal protein S30-A
y: 60S ribosomal protein L18-A
i: Suppressor protein STM1
F: 40S ribosomal protein S4-A
g: Ubiquitin
z: 60S ribosomal protein L19-A
G: 40S ribosomal protein S5
h: Guanine nucleotide-binding protein subunit beta-like protein
0: 60S ribosomal protein L20-A
H: 40S ribosomal protein S6-A
2: 60S ribosomal protein L21-A
I: 40S ribosomal protein S7-A
5: 60S ribosomal protein L22-A
J: 40S ribosomal protein S8-A
6: 60S ribosomal protein L23-A
K: 40S ribosomal protein S9-A
7: 60S ribosomal protein L24-A
L: 40S ribosomal protein S10-A
8: 60S ribosomal protein L25
M: 40S ribosomal protein S11-A
9: 60S ribosomal protein L26-A
O: 40S ribosomal protein S13
v: 60S ribosomal protein L15-A
AA: 60S ribosomal protein L27-A
P: 40S ribosomal protein S14-B
1: 25S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,269,3921252
Polymers3,120,49078
Non-polymers148,9021174
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CJ: 60S ribosomal protein L8-A
DJ: 60S ribosomal protein L35-A
s6: 40S ribosomal protein S6-A
CK: 60S ribosomal protein L9-A
DK: 60S ribosomal protein L36-A
s7: 40S ribosomal protein S7-A
CL: 60S ribosomal protein L10
DL: 60S ribosomal protein L37-A
s8: 40S ribosomal protein S8-A
CM: Large ribosomal subunit protein uL5B
DM: 60S ribosomal protein L38
s9: 40S ribosomal protein S9-A
CN: 60S ribosomal protein L13-A
DN: 60S ribosomal protein L39
c0: 40S ribosomal protein S10-A
CO: 60S ribosomal protein L14-A
DO: Ubiquitin-60S ribosomal protein L40
c1: 40S ribosomal protein S11-A
CP: 60S ribosomal protein L15-A
DP: Large ribosomal subunit protein eL41B
c3: 40S ribosomal protein S13
CQ: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L42-A
c4: 40S ribosomal protein S14-B
CR: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L43-A
c5: 40S ribosomal protein S15
CS: 60S ribosomal protein L18-A
p0: Large ribosomal subunit protein uL10
c6: 40S ribosomal protein S16-A
CT: 60S ribosomal protein L19-A
sM: Suppressor protein STM1
c7: 40S ribosomal protein S17-A
CU: 60S ribosomal protein L20-A
c8: 40S ribosomal protein S18-A
CV: 60S ribosomal protein L21-A
c9: 40S ribosomal protein S19-A
CW: 60S ribosomal protein L22-A
d0: Small ribosomal subunit protein uS10
CX: 60S ribosomal protein L23-A
d1: 40S ribosomal protein S21-A
CY: 60S ribosomal protein L24-A
d2: 40S ribosomal protein S22-A
CZ: 60S ribosomal protein L25
d3: 40S ribosomal protein S23-A
AR: 25S ribosomal RNA
DA: 60S ribosomal protein L26-A
d4: 40S ribosomal protein S24-A
AS: 5S ribosomal RNA
DB: 60S ribosomal protein L27-A
sR: 16S ribosomal RNA
d5: 40S ribosomal protein S25-A
AT: 5.8S ribosomal RNA
DC: 60S ribosomal protein L28
Rb: Guanine nucleotide-binding protein subunit beta-like protein
d6: Small ribosomal subunit protein eS26B
CD: 60S ribosomal protein L2-A
DD: 60S ribosomal protein L29
s0: 40S ribosomal protein S0-A
d7: 40S ribosomal protein S27-A
CE: 60S ribosomal protein L3
DE: 60S ribosomal protein L30
s1: 40S ribosomal protein S1-A
d8: 40S ribosomal protein S28-A
CF: 60S ribosomal protein L4-A
DF: 60S ribosomal protein L31-A
s2: 40S ribosomal protein S2
d9: Small ribosomal subunit protein uS14A
CG: 60S ribosomal protein L5
DG: 60S ribosomal protein L32
s3: Small ribosomal subunit protein uS3
e0: 40S ribosomal protein S30-A
CH: 60S ribosomal protein L6-A
DH: 60S ribosomal protein L33-A
s4: 40S ribosomal protein S4-A
CI: 60S ribosomal protein L7-A
DI: 60S ribosomal protein L34-A
s5: 40S ribosomal protein S5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,294,6451354
Polymers3,137,00678
Non-polymers157,6391276
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)302.090, 285.960, 433.310
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 3AS4ATAsRAR1

#1: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1329886537
#7: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1331532632
#58: RNA chain 16S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 874346701
#75: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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60S ribosomal protein ... , 38 types, 76 molecules ABDCCJpDJAIACDDCKqDKAJjCDADDECLrDLAKkCEAEDFDMALlCFAFDG...

#2: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#3: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#4: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84
#8: Protein 60S ribosomal protein L29 / Large ribosomal subunit protein eL29 / YL43


Mass: 6691.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747
#9: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#10: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#13: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45
#14: Protein 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#15: Protein 60S ribosomal protein L10 / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI- ...L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#16: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#19: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#20: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#22: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#25: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#26: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#27: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690
#28: Protein 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#31: Protein 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#32: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#33: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#37: Protein 60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#38: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#39: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#43: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#44: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#45: Protein 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX27
#48: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#49: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX25
#51: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#54: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82
#57: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#60: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#63: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#66: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41
#69: Protein 60S ribosomal protein L24-A / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#72: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#76: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#79: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6

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40S ribosomal protein ... , 26 types, 52 molecules Qc5s6HRc6s7ISc7s8JTc8s9KUc9c0Lc1MWd1c3OXd2c4P...

#5: Protein 40S ribosomal protein S15 / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 16031.907 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#6: Protein 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37
#11: Protein 40S ribosomal protein S16-A / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15877.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX51
#12: Protein 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786
#17: Protein 40S ribosomal protein S17-A / RP51A / Small ribosomal subunit protein eS17-A


Mass: 15820.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407
#18: Protein 40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39
#23: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX55
#24: Protein 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#29: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#30: Protein 40S ribosomal protein S10-A / Small ribosomal subunit protein eS10-A


Mass: 12757.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08745
#36: Protein 40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47
#41: Protein 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0V8
#42: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#46: Protein 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#47: Protein 40S ribosomal protein S14-B / RP59B / Small ribosomal subunit protein uS11-B


Mass: 14675.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39516
#50: Protein 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29
#53: Protein 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31
#56: Protein 40S ribosomal protein S25-A / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 12067.272 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#61: Protein 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28051.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#62: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997
#64: Protein 40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33442
#65: Protein 40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7605.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#67: Protein 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 27490.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#71: Protein 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33
#73: Protein 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35
#77: Protein 40S ribosomal protein S5 / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 25072.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783

-
Large ribosomal subunit protein ... , 3 types, 5 molecules CMsDPAOp0

#21: Protein Large ribosomal subunit protein uL5B / 60S ribosomal protein L11-B / L16 / RP39 / YL22


Mass: 19785.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E757
#40: Protein/peptide Large ribosomal subunit protein eL41B / 60S ribosomal protein L41-B / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX87
#52: Protein Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / A0 / L10e


Mass: 33770.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

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Protein , 4 types, 7 molecules DOANsMighRb

#34: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#55: Protein Suppressor protein STM1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / ...3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


Mass: 30048.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39015
#74: Protein Ubiquitin


Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05759
#78: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34841.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011

-
Small ribosomal subunit protein ... , 4 types, 8 molecules Vd0bd6ed9Es3

#35: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13929.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#59: Protein Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


Mass: 13480.886 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39939
#68: Protein Small ribosomal subunit protein uS14A / 40S ribosomal protein S29-A / S36 / YS29


Mass: 6675.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057
#70: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 / RP13 / YS3


Mass: 26542.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750

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Non-polymers , 7 types, 2862 molecules

#80: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 935 / Source method: obtained synthetically / Formula: H12N6Os
#81: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1490 / Source method: obtained synthetically / Formula: Mg
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#83: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#84: Chemical ChemComp-ZWB / (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione


Mass: 428.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30BrNO4 / Feature type: SUBJECT OF INVESTIGATION
#85: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3
#86: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30- ...Details: lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→150 Å / Num. obs: 3172226 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.995 / Rrim(I) all: 0.41 / Net I/σ(I): 23.52
Reflection shellResolution: 2.9→2.98 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 235166 / CC1/2: 0.12

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→95.96 Å / Cross valid method: FREE R-VALUE / σ(F): 0.8
RfactorNum. reflection% reflection
Rfree0.2301 -1.5 %
Rwork0.2185 --
obs-1597455 99.79 %
Displacement parametersBiso mean: 79.55 Å2
Refinement stepCycle: LAST / Resolution: 2.9→95.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms172844 220991 8132 412 402379

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