General information
PDB ID 3IYD
Title THREE-DIMENSIONAL EM STRUCTURE OF AN INTACT ACTIVATOR-DEPENDENT TRANSCRIPTION INITIATION COMPLEX
PDB header TRANSCRIPTION/DNA
Date 2009-08-01
Experimental method ELECTRON MICROSCOPY
Resolution (A) 19.8
Kind dna
Organism ESCHERICHIA COLI, ESCHERICHIA COLI K-12
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb3iyd.pdb ABCDEFGH IJ 0
Biounits:
3iyd.pdb1.pdb ABCDEFGH IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RNA_pol_A_CTD Domain P0A7Z4_243-309 7.8e-24 1 CL0198 A 243 309 J  H-Bb 
RNA_pol_A_bac Domain P0A7Z4_58-186 1.9e-23 1 No_clan A 58 186   
RNA_pol_L Domain P0A7Z4_29-228 3.6e-22 1 CL0509 A 29 228   
RNA_pol_A_bac Domain P0A7Z4_58-186 9.3e-24 1 No_clan B 58 185   
RNA_pol_L Domain P0A7Z4_29-228 1.3e-22 1 CL0509 B 29 228   
RNA_pol_Rpb2_6 Domain P0A8V2_717-1264 7.6e-163 1 CL0410 C 717 1264 J   
RNA_pol_Rpb2_3 Domain P0A8V2_513-581 1.4e-29 1 No_clan C 513 581   
RNA_pol_Rpb2_45 Domain P0A8V2_591-656 1.6e-27 1 No_clan C 591 656   
RNA_pol_Rpb2_7 Domain P0A8V2_1266-1342 2.4e-27 1 No_clan C 1266 1342 J   
RNA_pol_Rpb2_2 Domain P0A8V2_143-355 6.5e-26 1 No_clan C 151 454 I   
RNA_pol_Rpb1_1 Domain P0A8T7_15-342 1.1e-89 1 No_clan D 15 342 J   
RNA_pol_Rpb1_5 Domain P0A8T7_766-1317 6.1e-78 1 No_clan D 766 1317 J   
RNA_pol_Rpb1_2 Domain P0A8T7_386-486 4.3e-27 1 No_clan D 386 486 J   
RNA_pol_Rpb1_3 Domain P0A8T7_489-644 5.2e-27 1 No_clan D 489 644   
RNA_pol_Rpb1_4 Domain P0A8T7_673-764 1.5e-18 1 No_clan D 673 764   
RNA_pol_Rpb1_2 Domain P0A8T7_344-401 1.3e-07 1 No_clan D 344 401 J   
Sigma70_ner Domain P00579_137-348 1.4e-67 1 CL0123 F 137 348   
Sigma70_r2 Domain P00579_379-449 1.1e-21 1 CL0123 F 379 449 IJ   
Sigma70_r4 Domain P00579_547-600 6.1e-19 1 CL0123 F 547 600 IJ  H-Bb H-Mj L-Bb L-Mj 
cNMP_binding Domain P0ACJ8_21-110 3.4e-24 1 CL0029 G 20 109   
HTH_Crp_2 Domain P0ACJ8_142-206 2.6e-13 1 CL0123 G 141 206 IJ  H-Bb L-Bb 
cNMP_binding Domain P0ACJ8_21-110 3.4e-24 1 CL0029 H 20 109 IJ   
HTH_Crp_2 Domain P0ACJ8_142-206 2.6e-13 1 CL0123 H 141 206 IJ   
RNA_pol_Rpb2_1 Family P0A8V2_26-500 1.3e-58 1 No_clan C 26 500 I   
RNA_pol_Rpb6 Family P0A800_8-60 6e-17 1 No_clan E 8 60   
Sigma70_r3 Family P00579_458-535 8.3e-30 1 CL0123 F 458 535 J   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/B=1-329 C cytoplasm
A/B=1-329 C cytosol
A/B=1-329 C membrane
A/B=1-329 F DNA binding
A/B=1-329 F DNA-directed 5'-3' RNA polymerase activity
A/B=1-329 F protein dimerization activity
A/B=1-329 P transcription, DNA-templated
C=1-1342 C cytoplasm
C=1-1342 C cytosol
C=1-1342 C membrane
C=1-1342 F DNA binding
C=1-1342 F DNA-directed 5'-3' RNA polymerase activity
C=1-1342 F ribonucleoside binding
C=1-1342 P response to antibiotic
C=1-1342 P transcription, DNA-templated
D=1-1407 C cytoplasm
D=1-1407 C cytosol
D=1-1407 C membrane
D=1-1407 F DNA binding
D=1-1407 F DNA-directed 5'-3' RNA polymerase activity
D=1-1407 F magnesium ion binding
D=1-1407 F zinc ion binding
D=1-1407 P response to antibiotic
D=1-1407 P transcription, DNA-templated
E=2-91 C cytosol
E=2-91 C RNA polymerase complex
E=2-91 F DNA binding
E=2-91 F DNA-directed 5'-3' RNA polymerase activity
E=2-91 P protein-containing complex assembly
E=2-91 P transcription, DNA-templated
F=1-613 C cytosol
F=1-613 F DNA binding
F=1-613 F DNA-binding transcription factor activity
F=1-613 F sigma factor activity
F=1-613 P response to heat
F=1-613 P transcription initiation from bacterial-type RNA polymerase promoter
G/H=2-210 C cytosol
G/H=2-210 C protein-DNA complex
G/H=2-210 F AT DNA binding
G/H=2-210 F cAMP binding
G/H=2-210 F DNA binding, bending
G/H=2-210 F DNA-binding transcription factor activity
G/H=2-210 F identical protein binding
G/H=2-210 F sequence-specific DNA binding
G/H=2-210 P carbon catabolite repression of transcription
G/H=2-210 P negative regulation of transcription, DNA-templated
G/H=2-210 P positive regulation of transcription, DNA-templated
G/H=2-210 P transcription, DNA-templated
Sequences
Download file with secondary structure created by Stride  
3iyd.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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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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