General information
PDB ID 6RBD
Title STATE 1 OF YEAST TSR1-TAP RPS20-DELTALOOP PRE-40S PARTICLES
PDB header RIBOSOME
Date 2019-04-10
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.47
Kind rna
Organism SACCHAROMYCES CEREVISIAE S288C
Download
complex
View in
Jmol
Quick Links
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:
pdb6rbd.pdb beABCEGHIJLNVWXYcdhiklyFMOPQRSTZDU 2 0
Biounits:
6rbd.pdb1.pdb beABCEGHIJLNVWXYcdhiklyFMOPQRSTZDU 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 8.4e-23 1 No_clan D 105 188   
KH_2 Domain P05750_20-96 1.5e-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   
S4 Domain O13516_107-153 3.3e-12 1 CL0492 J 107 153 2   
AARP2CN Domain Q07381_234-309 1.2e-21 1 No_clan k 234 335   
Rio2_N Domain P40160_13-91 1e-29 1 CL0123 l 13 91 2   
Ribosomal_S17 Domain P0CX47_73-141 6.6e-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 1.4e-32 1 No_clan P 43 128 2   
Ribosomal_S8 Domain P0C0W1_5-130 5e-24 1 No_clan W 5 130 2   
RrnaAD Domain P41819_136-282 5.5e-30 1 CL0063 y 136 282 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_20-221 7.6e-88 1 No_clan B 20 221 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_20-56 5.4e-12 1 No_clan d 20 56 2   
Ribosomal_S4e Family P0CX35_95-169 2.1e-38 1 No_clan E 95 169 2   
40S_S4_C Family P0CX35_212-259 3.8e-26 1 No_clan E 212 259 2   
Ribosomal_S30 Family P0CX33_7-61 3.3e-11 1 No_clan e 11 61 2   
KOW Family P0CX35_177-211 3.8e-06 1 CL0107 E 177 211 2   
Ribosomal_S6e Family P0CX37_1-126 6.4e-58 1 No_clan G 1 126 2   
Ribosomal_S7e Family P26786_5-187 6.2e-80 1 CL0652 H 5 187 2   
Bystin Family P38333_252-390 2e-60 1 No_clan i 252 390 2   
Ribosomal_S8e Family P0CX39_2-184 1.8e-59 1 No_clan I 2 184 2   
RIBIOP_C Family Q07381_486-779 1.1e-106 1 CL0575 k 486 779 2   
RIO1 Family P40160_108-293 1.1e-33 1 CL0016 l 122 293 2   
Ribosomal_S17_N Family P0CX47_8-71 6.6e-32 1 No_clan L 8 71 2   
Ribosomal_S11 Family P06367_15-129 3.2e-46 1 CL0267 O 15 133 2   
Ribosomal_S9 Family P0CX51_11-129 9.9e-26 1 CL0329 Q 11 129 2   
Ribosomal_S17e Family P02407_2-126 6e-55 1 No_clan R 2 122 2   
Ribosomal_S13 Family P0CX55_16-105 7.7e-33 1 CL0303 S 16 105 2   
Ribosomal_S19e Family P07280_5-142 8.8e-54 1 CL0123 T 5 142 2   
Ribosomal_S10 Family P38701_23-109 3.5e-14 1 No_clan U 23 109 2   
Ribosomal_S21e Family P0C0V8_1-80 5.8e-40 1 No_clan V 1 80 2   
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_42-104 1.3e-24 1 CL0123 Z 42 104 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=1-225 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
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
h=1-274 C 90S preribosome
h=1-274 C cytoplasm
h=1-274 C nucleolus
h=1-274 C nucleus
h=1-274 F RNA binding
h=1-274 F unfolded protein binding
h=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)
h=1-274 P endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
h=1-274 P proteasome assembly
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)
i=1-483 C 90S preribosome
i=1-483 C cytoplasm
i=1-483 C nucleolus
i=1-483 C nucleus
i=1-483 C preribosome, small subunit precursor
i=1-483 F snoRNA binding
i=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)
i=1-483 P poly(A)+ mRNA export from nucleus
i=1-483 P rRNA processing
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=1-788 C 90S preribosome
k=1-788 C cytoplasm
k=1-788 C nucleolus
k=1-788 C nucleus
k=1-788 C preribosome, small subunit precursor
k=1-788 F GTP binding
k=1-788 F GTPase activity
k=1-788 F ribonucleoprotein complex binding
k=1-788 F U3 snoRNA binding
k=1-788 P endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
k=1-788 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
k=1-788 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
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
l=1-425 C cytoplasm
l=1-425 C cytoplasmic stress granule
l=1-425 C cytosol
l=1-425 C nucleus
l=1-425 C preribosome, small subunit precursor
l=1-425 F ATP binding
l=1-425 F metal ion binding
l=1-425 F protein kinase activity
l=1-425 F protein serine/threonine kinase activity
l=1-425 P maturation of SSU-rRNA
l=1-425 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
l=1-425 P positive regulation of RNA import into nucleus
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)
y=1-318 C 90S preribosome
y=1-318 C mitochondrial matrix
y=1-318 C nucleolus
y=1-318 C preribosome, small subunit precursor
y=1-318 F 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity
y=1-318 F RNA binding
y=1-318 F rRNA (adenine-N6,N6-)-dimethyltransferase activity
y=1-318 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
y=1-318 P rRNA methylation
y=1-318 P rRNA modification
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  
6rbd.pdb1.pdb:   [ download sequences in FASTA format ]
A (protein): 
Click "SHOW" for view sequence
b (protein): 
Click "SHOW" for view sequence
c (protein): 
Click "SHOW" for view sequence
d (protein): 
Click "SHOW" for view sequence
E (protein): 
Click "SHOW" for view sequence
F (protein): 
Click "SHOW" for view sequence
G (protein): 
Click "SHOW" for view sequence
H (protein): 
Click "SHOW" for view sequence
I (protein): 
Click "SHOW" for view sequence
J (protein): 
Click "SHOW" for view sequence
k (protein): 
Click "SHOW" for view sequence
l (protein): 
Click "SHOW" for view sequence
M (protein): 
Click "SHOW" for view sequence
N (protein): 
Click "SHOW" for view sequence
O (protein): 
Click "SHOW" for view sequence
P (protein): 
Click "SHOW" for view sequence
Q (protein): 
Click "SHOW" for view sequence
R (protein): 
Click "SHOW" for view sequence
S (protein): 
Click "SHOW" for view sequence
T (protein): 
Click "SHOW" for view sequence
U (protein): 
Click "SHOW" for view sequence
V (protein): 
Click "SHOW" for view sequence
W (protein): 
Click "SHOW" for view sequence
X (protein): 
Click "SHOW" for view sequence
y (protein): 
Click "SHOW" for view sequence
Z (protein): 
Click "SHOW" for view sequence
2 (rna): 
Click "SHOW" for view sequence
© NPIDB team 2003 - 2020

text