General information
PDB ID 5MY1
Title E. COLI EXPRESSOME
PDB header RIBOSOME
Date 2017-01-25
Experimental method ELECTRON MICROSCOPY
Resolution (A) 7.6
Kind rna
Organism ESCHERICHIA COLI K-12
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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:
pdb5my1.pdb CDEFGHIJKLMNOPQRSTBUVWXYZ A 0
Biounits:
5my1.pdb1.pdb CDEFGHIJKLMNOPQRSTBUVWXYZ A 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S3_C Domain P0A7V3_120-202 2e-40 1 No_clan C 119 201 A   
KH_2 Domain P0A7V3_38-111 7.3e-19 1 CL0007 C 37 110   
S4 Domain P0A7V8_96-143 1e-18 1 CL0492 D 95 142 A   
Ribosomal_S5_C Domain P0A7W1_87-157 3.7e-30 1 CL0329 E 86 156 A   
Ribosomal_S5 Domain P0A7W1_11-75 1e-29 1 CL0196 E 10 74 A   
Ribosomal_S6 Domain P02358_3-91 1.7e-28 1 No_clan F 3 91 A   
Ribosomal_S7 Domain P02359_2-149 3.6e-63 1 No_clan G 2 148 A   
Ribosomal_S8 Domain P0A7W7_5-130 3.8e-48 1 No_clan H 4 129 A   
Ribosomal_S10 Domain P0A7R5_7-101 1.9e-33 1 No_clan J 7 101 A   
Ribosomal_S15 Domain P0ADZ4_8-87 2.7e-37 1 CL0600 O 7 87 A   
Ribosomal_S17 Domain P0AG63_10-77 2.1e-34 1 CL0021 Q 9 76 A   
Ribosomal_S19 Domain P0A7U3_3-81 1.2e-35 1 No_clan S 2 80 A   
RNA_pol_A_bac Domain P0A7Z4_58-186 8.7e-24 1 No_clan V 58 178   
RNA_pol_L Domain P0A7Z4_29-228 1.1e-22 1 CL0509 V 29 228   
RNA_pol_A_bac Domain P0A7Z4_58-186 7.1e-24 1 No_clan W 58 186   
RNA_pol_L Domain P0A7Z4_29-228 9.8e-23 1 CL0509 W 29 228   
RNA_pol_Rpb2_6 Domain P0A8V2_717-1264 2.9e-160 1 CL0410 X 717 1264 A   
RNA_pol_Rpb2_3 Domain P0A8V2_513-581 1.7e-29 1 No_clan X 513 581   
RNA_pol_Rpb2_45 Domain P0A8V2_591-656 2.1e-27 1 No_clan X 591 656   
RNA_pol_Rpb2_7 Domain P0A8V2_1266-1342 4.4e-27 1 No_clan X 1266 1341   
RNA_pol_Rpb2_2 Domain P0A8V2_329-454 6e-15 1 No_clan X 329 454   
RNA_pol_Rpb2_2 Domain P0A8V2_151-276 2.6e-07 1 No_clan X 151 276   
RNA_pol_Rpb1_1 Domain P0A8T7_15-342 8e-90 1 No_clan Y 14 342   
RNA_pol_Rpb1_5 Domain P0A8T7_766-1317 1.3e-75 1 No_clan Y 766 1317   
RNA_pol_Rpb1_2 Domain P0A8T7_386-486 4.3e-27 1 No_clan Y 386 486   
RNA_pol_Rpb1_3 Domain P0A8T7_489-644 5.2e-27 1 No_clan Y 489 644   
RNA_pol_Rpb1_4 Domain P0A8T7_673-764 1.5e-18 1 No_clan Y 673 764   
RNA_pol_Rpb1_2 Domain P0A8T7_344-401 1.3e-07 1 No_clan Y 344 401   
Ribosomal_S2 Family P0A7V0_9-224 2.2e-93 1 CL0067 B 8 223 A   
Ribosomal_S4 Family P0A7V8_3-95 1.8e-32 1 CL0492 D 2 94 A   
Ribosomal_S9 Family P0A7X3_10-130 1.1e-46 1 CL0329 I 9 129 A   
Ribosomal_S11 Family P0A7R9_19-128 1.5e-54 1 CL0267 K 18 127 A   
Ribosom_S12_S23 Family P0A7S3_12-123 5.6e-43 1 CL0021 L 11 122 A   
Ribosomal_S13 Family P0A7S9_3-108 7.4e-34 1 CL0303 M 2 107 A   
Ribosomal_S14 Family P0AG59_47-100 1.1e-26 1 No_clan N 46 99 A   
Ribosomal_S16 Family P0A7T3_8-68 1.1e-24 1 No_clan P 8 68 A   
Ribosomal_S18 Family P0A7T7_20-68 1.4e-24 1 CL0123 R 19 67 A   
Ribosomal_S20p Family P0A7U7_3-84 3.7e-27 1 No_clan T 2 83 A   
Ribosomal_S21 Family P68679_4-54 1.3e-21 1 No_clan U 3 53 A   
RNA_pol_Rpb2_1 Family P0A8V2_26-500 2.5e-58 1 No_clan X 26 500   
RNA_pol_Rpb6 Family P0A800_8-60 4.1e-17 1 No_clan Z 8 60   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
B=2-241 C cytosolic small ribosomal subunit
B=2-241 F structural constituent of ribosome
B=2-241 F zinc ion binding
B=2-241 P ribosomal small subunit assembly
B=2-241 P translation
C=2-233 C cytosol
C=2-233 C cytosolic small ribosomal subunit
C=2-233 F mRNA binding
C=2-233 F rRNA binding
C=2-233 F structural constituent of ribosome
C=2-233 P ribosomal small subunit assembly
C=2-233 P translation
D=2-206 C cytosol
D=2-206 C cytosolic small ribosomal subunit
D=2-206 C small ribosomal subunit
D=2-206 F mRNA 5'-UTR binding
D=2-206 F rRNA binding
D=2-206 F structural constituent of ribosome
D=2-206 F translation repressor activity, mRNA regulatory element binding
D=2-206 P DNA-templated transcription, termination
D=2-206 P maintenance of translational fidelity
D=2-206 P negative regulation of translational initiation
D=2-206 P positive regulation of translational fidelity
D=2-206 P response to antibiotic
D=2-206 P ribosomal small subunit assembly
D=2-206 P transcription antitermination
E=2-167 C cytosol
E=2-167 C cytosolic small ribosomal subunit
E=2-167 F rRNA binding
E=2-167 F structural constituent of ribosome
E=2-167 P maintenance of translational fidelity
E=2-167 P response to antibiotic
E=2-167 P ribosomal small subunit assembly
E=2-167 P translation
F=1-135 C cytosol
F=1-135 C cytosolic small ribosomal subunit
F=1-135 F mRNA 5'-UTR binding
F=1-135 F small ribosomal subunit rRNA binding
F=1-135 F structural constituent of ribosome
F=1-135 P translation
G=2-179 C cytosol
G=2-179 C cytosolic small ribosomal subunit
G=2-179 C membrane
G=2-179 C ribosome
G=2-179 F mRNA binding
G=2-179 F rRNA binding
G=2-179 F structural constituent of ribosome
G=2-179 F tRNA binding
G=2-179 P negative regulation of translation
G=2-179 P ribosomal small subunit assembly
G=2-179 P translation
H=2-130 C cytosol
H=2-130 C cytosolic small ribosomal subunit
H=2-130 F rRNA binding
H=2-130 F structural constituent of ribosome
H=2-130 P regulation of mRNA stability
H=2-130 P regulation of translation
H=2-130 P ribosomal small subunit assembly
H=2-130 P translation
I=2-130 C cytosol
I=2-130 C cytosolic small ribosomal subunit
I=2-130 C small ribosomal subunit
I=2-130 F RNA binding
I=2-130 F structural constituent of ribosome
I=2-130 F tRNA binding
I=2-130 P translation
J=1-103 C cytosol
J=1-103 C cytosolic small ribosomal subunit
J=1-103 C small ribosomal subunit
J=1-103 F structural constituent of ribosome
J=1-103 F transcription antitermination factor activity, RNA binding
J=1-103 F tRNA binding
J=1-103 P transcription antitermination
J=1-103 P translation
K=2-129 C cytosol
K=2-129 C cytosolic small ribosomal subunit
K=2-129 F mRNA 5'-UTR binding
K=2-129 F small ribosomal subunit rRNA binding
K=2-129 F structural constituent of ribosome
K=2-129 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
K=2-129 P ribosomal small subunit assembly
K=2-129 P translation
L=2-124 C cytosol
L=2-124 C cytosolic small ribosomal subunit
L=2-124 C ribosome
L=2-124 F misfolded RNA binding
L=2-124 F rRNA binding
L=2-124 F structural constituent of ribosome
L=2-124 F tRNA binding
L=2-124 P Group I intron splicing
L=2-124 P maintenance of translational fidelity
L=2-124 P positive regulation of RNA splicing
L=2-124 P response to antibiotic
L=2-124 P RNA folding
L=2-124 P translation
M=2-118 C cytosol
M=2-118 C cytosolic small ribosomal subunit
M=2-118 C small ribosomal subunit
M=2-118 F rRNA binding
M=2-118 F structural constituent of ribosome
M=2-118 F tRNA binding
M=2-118 P translation
N=2-101 C cytosolic small ribosomal subunit
N=2-101 C small ribosomal subunit
N=2-101 F rRNA binding
N=2-101 F structural constituent of ribosome
N=2-101 P ribosomal small subunit assembly
N=2-101 P translation
O=1-89 C cytosol
O=1-89 C cytosolic small ribosomal subunit
O=1-89 F mRNA binding involved in posttranscriptional gene silencing
O=1-89 F rRNA binding
O=1-89 F small ribosomal subunit rRNA binding
O=1-89 F structural constituent of ribosome
O=1-89 P regulation of translation
O=1-89 P ribosomal small subunit assembly
O=1-89 P translation
P=1-82 C cytosolic small ribosomal subunit
P=1-82 C small ribosomal subunit
P=1-82 F endodeoxyribonuclease activity
P=1-82 F four-way junction DNA binding
P=1-82 F structural constituent of ribosome
P=1-82 P ribosomal small subunit assembly
P=1-82 P translation
Q=2-84 C cytosolic small ribosomal subunit
Q=2-84 F rRNA binding
Q=2-84 F small ribosomal subunit rRNA binding
Q=2-84 F structural constituent of ribosome
Q=2-84 P response to antibiotic
Q=2-84 P ribosomal small subunit assembly
Q=2-84 P translation
R=2-75 C cytosol
R=2-75 C cytosolic small ribosomal subunit
R=2-75 F mRNA 5'-UTR binding
R=2-75 F small ribosomal subunit rRNA binding
R=2-75 F structural constituent of ribosome
R=2-75 P translation
S=2-92 C cytosol
S=2-92 C cytosolic small ribosomal subunit
S=2-92 F rRNA binding
S=2-92 F structural constituent of ribosome
S=2-92 F tRNA binding
S=2-92 P ribosomal small subunit assembly
S=2-92 P translation
T=2-87 C cytosol
T=2-87 C cytosolic small ribosomal subunit
T=2-87 C small ribosomal subunit
T=2-87 F ornithine decarboxylase inhibitor activity
T=2-87 F small ribosomal subunit rRNA binding
T=2-87 F structural constituent of ribosome
T=2-87 P ribosomal small subunit assembly
T=2-87 P translation
U=1-71 C cytosol
U=1-71 C cytosolic small ribosomal subunit
U=1-71 F rRNA binding
U=1-71 F structural constituent of ribosome
U=1-71 P ribosomal small subunit assembly
U=1-71 P translation
V/W=1-329 C cytoplasm
V/W=1-329 C cytosol
V/W=1-329 C membrane
V/W=1-329 F DNA binding
V/W=1-329 F DNA-directed 5'-3' RNA polymerase activity
V/W=1-329 F protein dimerization activity
V/W=1-329 P transcription, DNA-templated
X=1-1342 C cytoplasm
X=1-1342 C cytosol
X=1-1342 C membrane
X=1-1342 F DNA binding
X=1-1342 F DNA-directed 5'-3' RNA polymerase activity
X=1-1342 F ribonucleoside binding
X=1-1342 P response to antibiotic
X=1-1342 P transcription, DNA-templated
Y=1-1407 C cytoplasm
Y=1-1407 C cytosol
Y=1-1407 C membrane
Y=1-1407 F DNA binding
Y=1-1407 F DNA-directed 5'-3' RNA polymerase activity
Y=1-1407 F magnesium ion binding
Y=1-1407 F zinc ion binding
Y=1-1407 P response to antibiotic
Y=1-1407 P transcription, DNA-templated
Z=1-91 C cytosol
Z=1-91 C RNA polymerase complex
Z=1-91 F DNA binding
Z=1-91 F DNA-directed 5'-3' RNA polymerase activity
Z=1-91 P protein-containing complex assembly
Z=1-91 P transcription, DNA-templated
Sequences
Download file with secondary structure created by Stride  
5my1.pdb1.pdb:   [ download sequences in FASTA format ]
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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A (rna): 
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