General information
PDB ID 6EML
Title CRYO-EM STRUCTURE OF A LATE PRE-40S RIBOSOMAL SUBUNIT FROM SACCHAROMYCES CEREVISIAE
PDB header RIBOSOME
Date 2017-10-02
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.6
Kind rna
Organism SACCHAROMYCES CEREVISIAE S288C
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6eml.pdb DBCEFHIKLNPQRSTUVWXYZabcdftgpre 2 0
Biounits:
6eml.pdb1.pdb DBCEFHIKLNPQRSTUVWXYZabcdftgpre 2 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S7 Domain P26783_76-225 4.5e-32 1 No_clan B 72 225 2   
Ribosomal_S8 Domain P0C0W1_5-130 5e-24 1 No_clan b 5 130 2   
Ribosomal_L7Ae Domain P48589_26-123 1.2e-22 1 CL0101 D 26 123 2   
Ribosomal_S19 Domain Q01855_43-128 1.6e-32 1 No_clan E 43 128 2   
Ribosomal_S27 Domain P05759_102-147 1.8e-25 1 CL0167 N 102 147 2   
Rio2_N Domain P40160_8-91 2.4e-29 1 CL0123 r 8 91 2   
Ribosomal_S5 Domain P25443_76-140 1.1e-26 1 CL0196 R 76 140 2   
Ribosomal_S5_C Domain P25443_159-230 4.9e-24 1 CL0329 R 159 230 2   
RS4NT Domain P0CX35_3-39 1.5e-19 1 No_clan S 3 39 2   
S4 Domain P0CX35_42-90 1.6e-08 1 CL0492 S 42 90 2   
AARP2CN Domain Q07381_234-309 1.5e-21 1 No_clan t 234 336 2   
S4 Domain O13516_107-153 3.3e-12 1 CL0492 W 107 153 2   
Ribosomal_S17 Domain P0CX47_73-141 8.4e-28 1 CL0021 X 73 141 2   
Ribosomal_S13_N Domain P05756_2-60 8.1e-28 1 No_clan Y 2 60 2   
Ribosomal_S15 Domain P05756_70-149 3.2e-15 1 CL0600 Y 70 149 2   
Ribosomal_S21e Family P0C0V8_1-80 5.8e-40 1 No_clan a 1 80 2   
Ribosom_S12_S23 Family P0CX29_31-144 2.1e-51 1 CL0021 c 31 144 2   
Ribosomal_S17e Family P02407_2-126 6.3e-46 1 No_clan C 2 122 2   
Ribosomal_S24e Family P0CX31_24-102 6.5e-35 1 No_clan d 24 102 2   
Bystin Family P38333_205-465 2.1e-116 1 No_clan e 205 465 2   
Ribosomal_S9 Family P0CX51_11-143 1.3e-32 1 CL0329 F 11 143 2   
Ribosomal_S27e Family P35997_28-82 5e-30 1 CL0167 f 28 82 2   
Ribosomal_S30 Family P0CX33_7-61 8.2e-29 1 No_clan g 3 61 2   
Ribosomal_S13 Family P0CX55_16-131 1.3e-47 1 CL0303 H 16 131 2   
Ribosomal_S19e Family P07280_5-142 8.8e-54 1 CL0123 I 5 142 2   
Ribosomal_S25 Family Q3E792_42-104 1.3e-24 1 CL0123 K 42 104 2   
Ribosomal_S28e Family P0C0X0_5-66 1.2e-32 1 CL0021 L 5 66 2   
Ribosomal_S2 Family P32905_110-183 2.9e-14 1 CL0067 P 111 183 2   
Ribosomal_S2 Family P32905_17-117 9.4e-10 1 CL0067 P 17 116 2   
Ribosomal_S3Ae Family P33442_20-221 7.6e-88 1 No_clan Q 20 221 2   
RIO1 Family P40160_108-288 3e-35 1 CL0016 r 108 287 2   
Ribosomal_S4e Family P0CX35_95-169 2.1e-38 1 No_clan S 95 169 2   
40S_S4_C Family P0CX35_212-259 3.8e-26 1 No_clan S 212 259 2   
KOW Family P0CX35_177-211 3.8e-06 1 CL0107 S 177 211 2   
RIBIOP_C Family Q07381_486-779 1.2e-106 1 CL0575 t 486 779 2   
Ribosomal_S6e Family P0CX37_1-126 6e-58 1 No_clan T 1 126 2   
Ribosomal_S7e Family P26786_5-187 6.2e-80 1 CL0652 U 5 187 2   
Ribosomal_S8e Family P0CX39_2-184 1.8e-59 1 No_clan V 2 184 2   
Ribosomal_S17_N Family P0CX47_8-71 8.4e-32 1 No_clan X 8 71 2   
Ribosomal_S11 Family P06367_15-129 3.2e-46 1 CL0267 Z 15 133 2   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
a=1-87 C cytosolic small ribosomal subunit
a=1-87 F structural constituent of ribosome
a=1-87 P cytoplasmic translation
a=1-87 P 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)
a=1-87 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
b=1-130 C cytosolic small ribosomal subunit
b=1-130 F structural constituent of ribosome
b=1-130 P cytoplasmic translation
B=1-225 C 90S preribosome
B=1-225 C cytosolic small ribosomal subunit
B=1-225 C ribosome
B=1-225 F mRNA binding
B=1-225 F rRNA binding
B=1-225 F structural constituent of ribosome
B=1-225 P cytoplasmic translation
B=1-225 P regulation of translational fidelity
B=1-225 P ribosomal small subunit assembly
B=1-225 P rRNA export from nucleus
B=1-225 P translation
C=1-136 C cytosolic small ribosomal subunit
C=1-136 F structural constituent of ribosome
C=1-136 P cytoplasmic translation
C=1-136 P ribosomal small subunit assembly
c=1-145 C cytosolic small ribosomal subunit
c=1-145 C ribosome
c=1-145 F structural constituent of ribosome
c=1-145 P maintenance of translational fidelity
c=1-145 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
c=1-145 P regulation of translational fidelity
c=1-145 P translation
d=1-135 C cytosolic small ribosomal subunit
d=1-135 C mitochondrion
d=1-135 F structural constituent of ribosome
d=1-135 P cytoplasmic translation
d=1-135 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D=1-143 C cytosolic small ribosomal subunit
D=1-143 F structural constituent of ribosome
D=1-143 P cytoplasmic translation
E=1-142 C cytosolic small ribosomal subunit
E=1-142 F RNA binding
E=1-142 F structural constituent of ribosome
E=1-142 P cytoplasmic translation
E=1-142 P ribosomal small subunit assembly
E=1-142 P rRNA export from nucleus
e=1-483 C 90S preribosome
e=1-483 C cytoplasm
e=1-483 C nucleolus
e=1-483 C nucleus
e=1-483 C preribosome, small subunit precursor
e=1-483 F snoRNA binding
e=1-483 P 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)
e=1-483 P poly(A)+ mRNA export from nucleus
e=1-483 P rRNA processing
F=1-143 C 90S preribosome
F=1-143 C cytosolic small ribosomal subunit
F=1-143 C small ribosomal subunit
F=1-143 F RNA binding
F=1-143 F structural constituent of ribosome
F=1-143 P cytoplasmic translation
F=1-143 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
f=1-82 C cytoplasm
f=1-82 C cytosolic small ribosomal subunit
f=1-82 F metal ion binding
f=1-82 F RNA binding
f=1-82 F structural constituent of ribosome
f=1-82 P cytoplasmic translation
f=1-82 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
f=1-82 P ribosomal small subunit assembly
g=1-63 C cytoplasmic stress granule
g=1-63 C cytosolic small ribosomal subunit
g=1-63 F structural constituent of ribosome
g=1-63 P cytoplasmic translation
H=1-146 C cytoplasm
H=1-146 C cytosol
H=1-146 C cytosolic small ribosomal subunit
H=1-146 C mitochondrion
H=1-146 C small ribosomal subunit
H=1-146 F rRNA binding
H=1-146 F structural constituent of ribosome
H=1-146 P cytoplasmic translation
H=1-146 P 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)
H=1-146 P rRNA export from nucleus
I=1-144 C cytosolic small ribosomal subunit
I=1-144 F RNA binding
I=1-144 F structural constituent of ribosome
I=1-144 P cytoplasmic translation
I=1-144 P ribosomal small subunit assembly
I=1-144 P ribosomal small subunit biogenesis
I=1-144 P rRNA export from nucleus
K=1-108 C cytosolic small ribosomal subunit
K=1-108 F structural constituent of ribosome
K=1-108 P cytoplasmic translation
L=1-67 C cytosolic small ribosomal subunit
L=1-67 F structural constituent of ribosome
L=1-67 P cytoplasmic translation
L=1-67 P maturation of SSU-rRNA
L=1-67 P positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
L=1-67 P ribosomal small subunit assembly
L=1-67 P rRNA export from nucleus
N=1-152 C cytoplasm
N=1-152 C cytosolic small ribosomal subunit
N=1-152 C nucleus
N=1-152 F metal ion binding
N=1-152 F protein tag
N=1-152 F structural constituent of ribosome
N=1-152 F ubiquitin protein ligase binding
N=1-152 P cytoplasmic translation
N=1-152 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S)
N=1-152 P modification-dependent protein catabolic process
N=1-152 P protein ubiquitination
N=1-152 P ribosomal small subunit assembly
N=1-152 P ribosome biogenesis
P=1-252 C 90S preribosome
P=1-252 C cytoplasmic stress granule
P=1-252 C cytosolic small ribosomal subunit
P=1-252 F structural constituent of ribosome
P=1-252 P cytoplasmic translation
P=1-252 P 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)
P=1-252 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
P=1-252 P ribosomal small subunit assembly
P=1-252 P rRNA export from nucleus
P=1-252 P translation
p=1-274 C 90S preribosome
p=1-274 C cytoplasm
p=1-274 C nucleolus
p=1-274 C nucleus
p=1-274 F RNA binding
p=1-274 F unfolded protein binding
p=1-274 P 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)
p=1-274 P endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p=1-274 P proteasome assembly
Q=1-255 C 90S preribosome
Q=1-255 C cytosol
Q=1-255 C cytosolic small ribosomal subunit
Q=1-255 F structural constituent of ribosome
Q=1-255 P cytoplasmic translation
Q=1-255 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
R=1-254 C cytosolic small ribosomal subunit
R=1-254 C nucleolus
R=1-254 C nucleoplasm
R=1-254 C small-subunit processome
R=1-254 F small ribosomal subunit rRNA binding
R=1-254 F structural constituent of ribosome
R=1-254 P positive regulation of translational fidelity
R=1-254 P rRNA export from nucleus
R=1-254 P rRNA methylation
R=1-254 P translation
r=1-425 C cytoplasm
r=1-425 C cytoplasmic stress granule
r=1-425 C cytosol
r=1-425 C nucleus
r=1-425 C preribosome, small subunit precursor
r=1-425 F ATP binding
r=1-425 F metal ion binding
r=1-425 F protein kinase activity
r=1-425 F protein serine/threonine kinase activity
r=1-425 P maturation of SSU-rRNA
r=1-425 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
r=1-425 P positive regulation of RNA import into nucleus
S=1-261 C 90S preribosome
S=1-261 C cytoplasm
S=1-261 C cytosolic small ribosomal subunit
S=1-261 F RNA binding
S=1-261 F rRNA binding
S=1-261 F structural constituent of ribosome
S=1-261 P cytoplasmic translation
S=1-261 P translation
T=1-236 C 90S preribosome
T=1-236 C cytosolic small ribosomal subunit
T=1-236 C nucleolus
T=1-236 C nucleoplasm
T=1-236 C small-subunit processome
T=1-236 F structural constituent of ribosome
T=1-236 P cytoplasmic translation
T=1-236 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
T=1-236 P rRNA methylation
t=1-788 C 90S preribosome
t=1-788 C cytoplasm
t=1-788 C nucleolus
t=1-788 C nucleus
t=1-788 C preribosome, small subunit precursor
t=1-788 F GTP binding
t=1-788 F GTPase activity
t=1-788 F ribonucleoprotein complex binding
t=1-788 F U3 snoRNA binding
t=1-788 P endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t=1-788 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t=1-788 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
U=1-190 C 90S preribosome
U=1-190 C cytosolic small ribosomal subunit
U=1-190 C nucleolus
U=1-190 C nucleoplasm
U=1-190 C small-subunit processome
U=1-190 F structural constituent of ribosome
U=1-190 P cytoplasmic translation
U=1-190 P ribosomal small subunit biogenesis
U=1-190 P ribosome biogenesis
U=1-190 P rRNA methylation
U=1-190 P rRNA processing
V=1-200 C 90S preribosome
V=1-200 C cytosolic small ribosomal subunit
V=1-200 F structural constituent of ribosome
V=1-200 P cytoplasmic translation
V=1-200 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
W=1-197 C 90S preribosome
W=1-197 C cytoplasm
W=1-197 C cytosolic small ribosomal subunit
W=1-197 C nucleolus
W=1-197 C nucleoplasm
W=1-197 C small ribosomal subunit
W=1-197 C small-subunit processome
W=1-197 F rRNA binding
W=1-197 F structural constituent of ribosome
W=1-197 P cytoplasmic translation
W=1-197 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
W=1-197 P positive regulation of translational fidelity
W=1-197 P rRNA methylation
X=1-156 C 90S preribosome
X=1-156 C cytosolic small ribosomal subunit
X=1-156 F rRNA binding
X=1-156 F structural constituent of ribosome
X=1-156 P cytoplasmic translation
X=1-156 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
X=1-156 P ribosomal small subunit assembly
Y=1-151 C 90S preribosome
Y=1-151 C cytosolic small ribosomal subunit
Y=1-151 C nucleolus
Y=1-151 F small ribosomal subunit rRNA binding
Y=1-151 F structural constituent of ribosome
Y=1-151 P cytoplasmic translation
Y=1-151 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Z=1-137 C 90S preribosome
Z=1-137 C cytosolic small ribosomal subunit
Z=1-137 C nucleolus
Z=1-137 C nucleoplasm
Z=1-137 C small-subunit processome
Z=1-137 F mRNA 5'-UTR binding
Z=1-137 F mRNA binding
Z=1-137 F small ribosomal subunit rRNA binding
Z=1-137 F structural constituent of ribosome
Z=1-137 P cytoplasmic translation
Z=1-137 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Z=1-137 P ribosomal small subunit assembly
Z=1-137 P rRNA methylation
Z=1-137 P translation
Sequences
Download file with secondary structure created by Stride  
6eml.pdb1.pdb:   [ download sequences in FASTA format ]
a (protein): 
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b (protein): 
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c (protein): 
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d (protein): 
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e (protein): 
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f (protein): 
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g (protein): 
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H (protein): 
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I (protein): 
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K (protein): 
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L (protein): 
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N (protein): 
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p (protein): 
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Q (protein): 
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R (protein): 
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S (protein): 
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T (protein): 
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U (protein): 
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V (protein): 
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W (protein): 
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X (protein): 
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Y (protein): 
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Z (protein): 
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2 (rna): 
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