General information
PDB ID 6RBE
Title STATE 2 OF YEAST TSR1-TAP RPS20-DELTALOOP PRE-40S PARTICLES
PDB header RIBOSOME
Date 2019-04-10
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.8
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:
pdb6rbe.pdb ABCEGHIJLNORVWXYbdeDFKMPQSTUZcfg 2 0
Biounits:
6rbe.pdb1.pdb ABCEGHIJLNORVWXYbdeDFKMPQSTUZcfg 2 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S5 Domain P25443_76-140 1.1e-26 1 CL0196 C 76 140 2   
Ribosomal_S5_C Domain P25443_159-230 4.8e-24 1 CL0329 C 159 230 2   
Ribosomal_S3_C Domain P05750_105-188 1.3e-22 1 No_clan D 105 188 2   
KH_2 Domain P05750_20-96 2.2e-11 1 CL0007 D 20 96 2   
RS4NT Domain P0CX35_3-39 1.5e-19 1 No_clan E 3 39 2   
S4 Domain P0CX35_42-90 1.6e-08 1 CL0492 E 42 90 2   
Ribosomal_S7 Domain P26783_76-225 4.4e-37 1 No_clan F 72 225 2   
Ribosomal_S27 Domain P05759_102-147 1.8e-25 1 CL0167 f 102 147 2   
S4 Domain O13516_107-153 3.3e-12 1 CL0492 J 107 153 2   
S10_plectin Domain Q08745_3-95 1.1e-42 1 No_clan K 3 95 2   
Ribosomal_S17 Domain P0CX47_73-141 8.4e-28 1 CL0021 L 73 141 2   
Ribosomal_L7Ae Domain P48589_26-123 1.2e-22 1 CL0101 M 26 123 2   
Ribosomal_S13_N Domain P05756_2-60 8.1e-28 1 No_clan N 2 60 2   
Ribosomal_S15 Domain P05756_70-149 3.2e-15 1 CL0600 N 70 149 2   
Ribosomal_S19 Domain Q01855_43-128 1.9e-32 1 No_clan P 43 128 2   
Ribosomal_S8 Domain P0C0W1_5-130 5e-24 1 No_clan W 5 130 2   
Ribosomal_S2 Family P32905_110-183 2.9e-14 1 CL0067 A 111 183 2   
Ribosomal_S2 Family P32905_17-117 9.4e-10 1 CL0067 A 17 116 2   
Ribosomal_S3Ae Family P33442_107-219 3.7e-43 1 No_clan B 107 219 2   
Ribosomal_S27e Family P35997_28-82 5e-30 1 CL0167 b 28 82 2   
Ribosomal_S28e Family Q3E7X9_5-66 1.2e-32 1 CL0021 c 5 66 2   
Ribosomal_S14 Family P41057_6-56 1.3e-15 1 No_clan d 6 56 2   
Ribosomal_S4e Family P0CX35_95-169 2.1e-38 1 No_clan E 95 169 2   
Ribosomal_S30 Family P0CX33_7-61 8.2e-29 1 No_clan e 3 61 2   
40S_S4_C Family P0CX35_212-259 3.8e-26 1 No_clan E 212 259 2   
KOW Family P0CX35_177-211 3.8e-06 1 CL0107 E 177 211 2   
Ribosomal_S6e Family P0CX37_1-126 6e-58 1 No_clan G 1 126 2   
Ribosomal_S7e Family P26786_5-187 6.2e-80 1 CL0652 H 5 187 2   
Ribosomal_S8e Family P0CX39_2-184 1.8e-59 1 No_clan I 2 184 2   
Ribosomal_S17_N Family P0CX47_8-71 8.4e-32 1 No_clan L 8 71 2   
Ribosomal_S9 Family P0CX51_11-143 1.3e-32 1 CL0329 Q 11 143 2   
Ribosomal_S17e Family P02407_2-126 3.2e-54 1 No_clan R 2 122 2   
Ribosomal_S13 Family P0CX55_16-144 5e-57 1 CL0303 S 16 144 2   
Ribosomal_S19e Family P07280_5-142 8.8e-54 1 CL0123 T 5 142 2   
Ribosomal_S10 Family P38701_23-117 3.3e-17 1 No_clan U 23 117 2   
Ribosomal_S21e Family P0C0V8_1-80 5.8e-40 1 No_clan V 1 80   
Ribosom_S12_S23 Family P0CX29_31-144 2.1e-51 1 CL0021 X 31 144 2   
Ribosomal_S24e Family P0CX31_24-102 6.5e-35 1 No_clan Y 24 102 2   
Ribosomal_S25 Family Q3E792_36-104 7.5e-27 1 CL0123 Z 36 104 2   
WD40 Repeat P38011_8-46 3e-07 1 CL0186 g 55 93 2   
WD40 Repeat P38011_280-314 1.8e-06 1 CL0186 g 186 224 2   
WD40 Repeat P38011_280-314 9.1e-06 1 CL0186 g 97 135 2   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=1-252 C 90S preribosome
A=1-252 C cytoplasmic stress granule
A=1-252 C cytosolic small ribosomal subunit
A=1-252 F structural constituent of ribosome
A=1-252 P cytoplasmic translation
A=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)
A=1-252 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A=1-252 P ribosomal small subunit assembly
A=1-252 P rRNA export from nucleus
A=1-252 P translation
B=1-255 C 90S preribosome
B=1-255 C cytosol
B=1-255 C cytosolic small ribosomal subunit
B=1-255 F structural constituent of ribosome
B=1-255 P cytoplasmic translation
B=1-255 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
b=1-82 C cytoplasm
b=1-82 C cytosolic small ribosomal subunit
b=1-82 F metal ion binding
b=1-82 F RNA binding
b=1-82 F structural constituent of ribosome
b=1-82 P cytoplasmic translation
b=1-82 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
b=1-82 P ribosomal small subunit assembly
C=1-254 C cytosolic small ribosomal subunit
C=1-254 C nucleolus
C=1-254 C nucleoplasm
C=1-254 C small-subunit processome
C=1-254 F small ribosomal subunit rRNA binding
C=1-254 F structural constituent of ribosome
C=1-254 P positive regulation of translational fidelity
C=1-254 P rRNA export from nucleus
C=1-254 P rRNA methylation
C=1-254 P translation
c=1-67 C cytosolic small ribosomal subunit
c=1-67 F structural constituent of ribosome
c=1-67 P cytoplasmic translation
c=1-67 P maturation of SSU-rRNA
c=1-67 P positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
c=1-67 P ribosomal small subunit assembly
c=1-67 P rRNA export from nucleus
D=1-240 C 90S preribosome
D=1-240 C cytosolic small ribosomal subunit
D=1-240 C nucleus
D=1-240 C preribosome, small subunit precursor
D=1-240 F DNA-(apurinic or apyrimidinic site) endonuclease activity
D=1-240 F protein kinase A catalytic subunit binding
D=1-240 F RNA binding
D=1-240 F structural constituent of ribosome
D=1-240 P cytoplasmic translation
D=1-240 P ribosomal small subunit export from nucleus
D=1-240 P rRNA export from nucleus
d=1-56 C cytosolic small ribosomal subunit
d=1-56 F structural constituent of ribosome
d=1-56 F zinc ion binding
d=1-56 P cytoplasmic translation
E=1-261 C 90S preribosome
E=1-261 C cytoplasm
E=1-261 C cytosolic small ribosomal subunit
E=1-261 F RNA binding
E=1-261 F rRNA binding
E=1-261 F structural constituent of ribosome
E=1-261 P cytoplasmic translation
E=1-261 P translation
e=1-63 C cytoplasmic stress granule
e=1-63 C cytosolic small ribosomal subunit
e=1-63 F structural constituent of ribosome
e=1-63 P cytoplasmic translation
f=1-152 C cytoplasm
f=1-152 C cytosolic small ribosomal subunit
f=1-152 C nucleus
f=1-152 F metal ion binding
f=1-152 F protein tag
f=1-152 F structural constituent of ribosome
f=1-152 F ubiquitin protein ligase binding
f=1-152 P cytoplasmic translation
f=1-152 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S)
f=1-152 P modification-dependent protein catabolic process
f=1-152 P protein ubiquitination
f=1-152 P ribosomal small subunit assembly
f=1-152 P ribosome biogenesis
F=1-225 C 90S preribosome
F=1-225 C cytosolic small ribosomal subunit
F=1-225 C ribosome
F=1-225 F mRNA binding
F=1-225 F rRNA binding
F=1-225 F structural constituent of ribosome
F=1-225 P cytoplasmic translation
F=1-225 P regulation of translational fidelity
F=1-225 P ribosomal small subunit assembly
F=1-225 P rRNA export from nucleus
F=1-225 P translation
G=1-236 C 90S preribosome
G=1-236 C cytosolic small ribosomal subunit
G=1-236 C nucleolus
G=1-236 C nucleoplasm
G=1-236 C small-subunit processome
G=1-236 F structural constituent of ribosome
G=1-236 P cytoplasmic translation
G=1-236 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
G=1-236 P rRNA methylation
g=1-319 C cytoplasm
g=1-319 C cytosol
g=1-319 C cytosolic small ribosomal subunit
g=1-319 C nucleus
g=1-319 F enzyme binding
g=1-319 F G-protein alpha-subunit binding
g=1-319 F GDP-dissociation inhibitor activity
g=1-319 F protein kinase C binding
g=1-319 F ribosome binding
g=1-319 P G protein-coupled receptor signaling pathway
g=1-319 P invasive growth in response to glucose limitation
g=1-319 P mRNA destabilization
g=1-319 P negative regulation of gene expression
g=1-319 P negative regulation of glucose mediated signaling pathway
g=1-319 P negative regulation of translation
g=1-319 P negative regulation of translational frameshifting
g=1-319 P positive regulation of protein phosphorylation
g=1-319 P protein localization
g=1-319 P regulation of cellular response to stress
g=1-319 P rescue of stalled ribosome
H=1-190 C 90S preribosome
H=1-190 C cytosolic small ribosomal subunit
H=1-190 C nucleolus
H=1-190 C nucleoplasm
H=1-190 C small-subunit processome
H=1-190 F structural constituent of ribosome
H=1-190 P cytoplasmic translation
H=1-190 P ribosomal small subunit biogenesis
H=1-190 P ribosome biogenesis
H=1-190 P rRNA methylation
H=1-190 P rRNA processing
I=1-200 C 90S preribosome
I=1-200 C cytosolic small ribosomal subunit
I=1-200 F structural constituent of ribosome
I=1-200 P cytoplasmic translation
I=1-200 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
J=1-197 C 90S preribosome
J=1-197 C cytoplasm
J=1-197 C cytosolic small ribosomal subunit
J=1-197 C nucleolus
J=1-197 C nucleoplasm
J=1-197 C small ribosomal subunit
J=1-197 C small-subunit processome
J=1-197 F rRNA binding
J=1-197 F structural constituent of ribosome
J=1-197 P cytoplasmic translation
J=1-197 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
J=1-197 P positive regulation of translational fidelity
J=1-197 P rRNA methylation
K=1-105 C cytosolic small ribosomal subunit
K=1-105 F RNA binding
K=1-105 F structural constituent of ribosome
K=1-105 P cellular response to amino acid starvation
K=1-105 P cytoplasmic translation
K=1-105 P positive regulation of protein kinase activity
K=1-105 P ribosomal small subunit assembly
K=1-105 P rRNA export from nucleus
L=1-156 C 90S preribosome
L=1-156 C cytosolic small ribosomal subunit
L=1-156 F rRNA binding
L=1-156 F structural constituent of ribosome
L=1-156 P cytoplasmic translation
L=1-156 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
L=1-156 P ribosomal small subunit assembly
M=1-143 C cytosolic small ribosomal subunit
M=1-143 F structural constituent of ribosome
M=1-143 P cytoplasmic translation
N=1-151 C 90S preribosome
N=1-151 C cytosolic small ribosomal subunit
N=1-151 C nucleolus
N=1-151 F small ribosomal subunit rRNA binding
N=1-151 F structural constituent of ribosome
N=1-151 P cytoplasmic translation
N=1-151 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
O=1-137 C 90S preribosome
O=1-137 C cytosolic small ribosomal subunit
O=1-137 C nucleolus
O=1-137 C nucleoplasm
O=1-137 C small-subunit processome
O=1-137 F mRNA 5'-UTR binding
O=1-137 F mRNA binding
O=1-137 F small ribosomal subunit rRNA binding
O=1-137 F structural constituent of ribosome
O=1-137 P cytoplasmic translation
O=1-137 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
O=1-137 P ribosomal small subunit assembly
O=1-137 P rRNA methylation
O=1-137 P translation
P=1-142 C cytosolic small ribosomal subunit
P=1-142 F RNA binding
P=1-142 F structural constituent of ribosome
P=1-142 P cytoplasmic translation
P=1-142 P ribosomal small subunit assembly
P=1-142 P rRNA export from nucleus
Q=1-143 C 90S preribosome
Q=1-143 C cytosolic small ribosomal subunit
Q=1-143 C small ribosomal subunit
Q=1-143 F RNA binding
Q=1-143 F structural constituent of ribosome
Q=1-143 P cytoplasmic translation
Q=1-143 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
R=1-136 C cytosolic small ribosomal subunit
R=1-136 F structural constituent of ribosome
R=1-136 P cytoplasmic translation
R=1-136 P ribosomal small subunit assembly
S=1-146 C cytoplasm
S=1-146 C cytosol
S=1-146 C cytosolic small ribosomal subunit
S=1-146 C mitochondrion
S=1-146 C small ribosomal subunit
S=1-146 F rRNA binding
S=1-146 F structural constituent of ribosome
S=1-146 P cytoplasmic translation
S=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)
S=1-146 P rRNA export from nucleus
T=1-144 C cytosolic small ribosomal subunit
T=1-144 F RNA binding
T=1-144 F structural constituent of ribosome
T=1-144 P cytoplasmic translation
T=1-144 P ribosomal small subunit assembly
T=1-144 P ribosomal small subunit biogenesis
T=1-144 P rRNA export from nucleus
U=1-121 C cytosolic small ribosomal subunit
U=1-121 C small ribosomal subunit
U=1-121 F mRNA binding
U=1-121 F structural constituent of ribosome
U=1-121 P cytoplasmic translation
U=1-121 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
V=1-87 C cytosolic small ribosomal subunit
V=1-87 F structural constituent of ribosome
V=1-87 P cytoplasmic translation
V=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)
V=1-87 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
W=1-130 C cytosolic small ribosomal subunit
W=1-130 F structural constituent of ribosome
W=1-130 P cytoplasmic translation
X=1-145 C cytosolic small ribosomal subunit
X=1-145 C ribosome
X=1-145 F structural constituent of ribosome
X=1-145 P maintenance of translational fidelity
X=1-145 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
X=1-145 P regulation of translational fidelity
X=1-145 P translation
Y=1-135 C cytosolic small ribosomal subunit
Y=1-135 C mitochondrion
Y=1-135 F structural constituent of ribosome
Y=1-135 P cytoplasmic translation
Y=1-135 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Z=1-108 C cytosolic small ribosomal subunit
Z=1-108 F structural constituent of ribosome
Z=1-108 P cytoplasmic translation
Sequences
Download file with secondary structure created by Stride  
6rbe.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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J (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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N (protein): 
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O (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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