General information
PDB ID 5FMF
Title THE P-LOBE OF RNA POLYMERASE II PRE-INITIATION COMPLEX
PDB header TRANSCRIPTION
Date 2015-11-03
Experimental method ELECTRON MICROSCOPY
Resolution (A) 6
Kind dna
Organism SACCHAROMYCES CEREVISIAE
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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:
pdb5fmf.pdb 12ABCDEFGHIJKLMOPQRSUVWXY NT 0
Biounits:
5fmf.pdb1.pdb 12ABCDEFGHIJKLMOPQRSUVWXY NT 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
ERCC3_RAD25_C Domain Q00578_549-785 3.1e-121 1 CL0023 1 535 784 T  L-Bb 
TFIIS_M Domain P07273_146-256 7.8e-25 1 No_clan 2 146 256   
TFIIS_C Domain P07273_269-307 1.3e-17 1 CL0167 2 269 307   
RNA_pol_Rpb1_1 Domain P04050_11-340 3.2e-114 1 No_clan A 11 340 T  L-Bb 
RNA_pol_Rpb1_5 Domain P04050_807-1397 2.7e-92 1 No_clan A 807 1397   
RNA_pol_Rpb1_2 Domain P04050_342-507 1.7e-77 1 No_clan A 342 507   
RNA_pol_Rpb1_6 Domain P04050_873-1056 2.4e-63 1 No_clan A 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.9e-47 1 No_clan A 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 3.2e-37 1 No_clan A 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 5.3e-35 1 No_clan A 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 1.6e-122 1 CL0410 B 752 1124   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.4e-51 1 No_clan B 219 407 T   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.8e-33 1 No_clan B 1126 1219   
RNA_pol_Rpb2_4 Domain P08518_580-641 1.6e-25 1 No_clan B 580 641   
RNA_pol_Rpb2_3 Domain P08518_481-545 3.4e-20 1 No_clan B 481 545   
RNA_pol_Rpb2_5 Domain P08518_681-745 1.4e-19 1 No_clan B 681 745   
RNA_pol_A_bac Domain P16370_49-171 7.3e-32 1 No_clan C 49 171   
RNA_pol_L Domain P16370_19-255 6.6e-19 1 CL0509 C 19 255   
RNA_pol_Rpb5_C Domain P20434_142-214 1.6e-31 1 No_clan E 142 214   
RNA_pol_Rpb5_N Domain P20434_6-100 1.1e-29 1 CL0236 E 6 100   
S1 Domain P34087_80-161 6.2e-18 1 CL0021 G 80 161   
SHS2_Rpb7-N Domain P34087_8-79 2.6e-16 1 CL0319 G 8 79   
RNA_POL_M_15KD Domain P27999_4-41 1.2e-17 1 CL0167 I 4 41   
TFIIS_C Domain P27999_73-111 0.000000000000013 1 CL0167 I 73 111   
RNA_pol_N Domain P22139_1-60 5.4e-30 1 No_clan J 1 60   
RNA_pol_L_2 Domain P38902_30-104 1.6e-24 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain P40422_29-60 1.9e-16 1 CL0167 L 29 60   
TFIIA_gamma_C Domain P32774_61-118 2.5e-24 1 No_clan O 56 118   
TFIIA_gamma_N Domain P32774_6-53 1.2e-22 1 No_clan O 6 53   
TFIIB Domain P29055_133-203 1.4e-28 1 CL0065 P 133 203   
TF_Zn_Ribbon Domain P29055_22-66 0.00000000000055 1 CL0167 P 22 66   
TFIIB Domain P29055_239-309 0.00000000000062 1 CL0065 P 230 309 T   
TBP Domain P13393_154-237 4.3e-33 1 CL0407 Q 154 237 NT   
TBP Domain P13393_64-146 1.3e-32 1 CL0407 Q 64 146 NT   
TF_Zn_Ribbon Domain P36100_122-160 0.00000008 1 CL0167 R 122 160   
TFIIE_beta Domain P36145_125-186 0.0000000000000018 1 CL0123 S 125 186   
Helicase_C_2 Domain P06839_526-699 5.7e-26 1 CL0023 Y 526 702   
HBB Domain P06839_287-415 3.8e-19 1 No_clan Y 264 491   
ResIII Family Q00578_359-519 2.5e-16 1 CL0023 1 359 519   
RNA_pol_Rpb2_1 Family P08518_42-455 1.8e-74 1 No_clan B 42 455 T   
RNA_pol_Rpb4 Family P20433_49-218 8.6e-39 1 CL0426 D 49 218   
RNA_pol_Rpb6 Family P20435_79-132 7.3e-18 1 No_clan F 79 132   
RNA_pol_Rpb8 Family P20436_7-146 2.1e-42 1 CL0021 H 7 146   
TFIIA Family P32773_228-285 5.7e-23 1 No_clan M 61 285 T   
TFIIA Family P32773_9-61 2e-18 1 No_clan M 9 230   
TFIIE_alpha Family P36100_12-95 5.4e-23 1 CL0123 R 12 120   
TFIIF_alpha Family P41895_293-417 0.000000000000018 1 CL0123 U 95 417   
TFIIF_beta Family P41896_292-356 2e-31 1 CL0123 V 227 356 NT  H-Bb H-Mj L-Bb L-Mj 
TFIIF_beta Family 1.7e-25 1 CL0123 V 58 212
Tau95 Family 0.00061 0 No_clan V 79 350 NT
Tfb5 Family Q3E7C1_2-64 2.2e-24 1 No_clan X 2 64 N  L-Bb 
DEAD_2 Family P06839_71-257 1.5e-53 1 CL0023 Y 71 257   
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
5fmf.pdb1.pdb:   [ download sequences in FASTA format ]
N (dna): 
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T (dna): 
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1 (protein): 
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2 (protein): 
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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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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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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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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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