General information
PDB ID 5SVA
Title MEDIATOR-RNA POLYMERASE II PRE-INITIATION COMPLEX
PDB header TRANSCRIPTION, TRANSFERASE/DNA
Date 2016-08-05
Experimental method ELECTRON MICROSCOPY
Resolution (A) 15.3
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:
pdb5sva.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijkn lm 0
Biounits:
5sva.pdb1.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijkn lm 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RNA_pol_Rpb1_1 Domain P04050_11-340 3.2e-114 1 No_clan A 11 340 m   
RNA_pol_Rpb1_5 Domain P04050_807-1397 2.7e-92 1 No_clan A 807 1397   
RNA_pol_Rpb1_2 Domain 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   
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   
TFIIB Domain P29055_133-203 5.8e-29 1 CL0065 c 133 203   
RNA_pol_L Domain P16370_19-255 6.6e-19 1 CL0509 C 19 255   
TF_Zn_Ribbon Domain P29055_22-66 0.00000000000027 1 CL0167 c 22 66   
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   
TFIIA_gamma_C Domain P32774_61-118 2.5e-24 1 No_clan e 56 118   
TFIIA_gamma_N Domain P32774_6-53 1.2e-22 1 No_clan e 6 53   
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   
TF_Zn_Ribbon Domain P36100_122-160 0.00000008 1 CL0167 h 122 160   
RNA_POL_M_15KD Domain P27999_4-41 1.2e-17 1 CL0167 I 4 41   
TFIIE_beta Domain P36145_125-186 0.0000000000000011 1 CL0123 i 125 186   
TFIIS_C Domain P27999_73-111 0.000000000000013 1 CL0167 I 73 111   
TBP Domain P13393_154-237 4.3e-33 1 CL0407 j 154 237 lm   
TBP Domain P13393_64-146 1.3e-32 1 CL0407 j 64 146 lm   
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   
Med18 Domain P32585_3-299 4.4e-51 1 CL0273 Q 3 299   
Helicase_C_2 Domain P06839_526-699 1.8e-30 1 CL0023 Y 526 703   
HBB Domain P06839_270-415 0.00000000000021 1 No_clan Y 295 491   
ERCC3_RAD25_C Domain Q00578_549-785 2.2e-120 1 CL0023 Z 535 784   
RNA_pol_Rpb2_1 Family P08518_42-455 1.8e-74 1 No_clan B 42 455   
Tfb5 Family Q3E7C1_2-64 2.2e-24 1 No_clan b 2 64   
RNA_pol_Rpb4 Family P20433_49-218 8.6e-39 1 CL0426 D 49 218   
TFIIA Family P32773_228-285 5.7e-23 1 No_clan d 61 285 lm   
TFIIA Family P32773_9-61 2e-18 1 No_clan d 9 230   
RNA_pol_Rpb6 Family P20435_79-132 7.3e-18 1 No_clan F 79 132   
TFIIF_alpha Family P41895_327-415 0.00000000035 1 CL0123 f 113 417 m  L-Bb 
TFIIF_beta Family P41896_292-356 2.3e-31 1 CL0123 g 291 356   
TFIIF_beta Family 1.4e-24 1 CL0123 g 58 211
Tau95 Family 0.00041 0 No_clan g 79 350
RNA_pol_Rpb8 Family 2.1e-42 1 CL0021 H 7 146
TFIIE_alpha Family P36100_12-95 5.4e-23 1 CL0123 h 12 120   
Med6 Family P38782_9-195 1e-49 1 No_clan M 9 192   
YEATS Family P35189_29-111 8.7e-20 1 CL0154 n 29 111   
Med8 Family P38304_31-210 6.5e-17 1 No_clan N 30 208   
BET Family P35189_180-240 0.0000039 1 No_clan n 137 240   
Med11 Family Q99278_7-104 0.000000000001 1 No_clan O 7 114   
Med17 Family P32569_182-569 7e-150 1 No_clan P 182 569   
Med20 Family P34162_2-209 8.8e-43 1 CL0273 R 3 209   
Med22 Family P32570_8-117 2.7e-16 1 No_clan S 8 119   
Med4 Family Q12343_67-127 0.0000000013 1 No_clan T 67 127   
Med7 Family 1.4e-35 1 No_clan U 108 203
Med7 Family 0.00000000000069 1 No_clan U 11 114
Med9 Family P33308_64-145 5.8e-25 1 No_clan V 65 147   
Med21 Family P47822_3-131 3.4e-36 1 No_clan W 3 131   
Med9 Family 0.00039 0 No_clan W 26 107
Med31 Family P38633_20-106 1.3e-25 1 No_clan X 20 101   
DEAD_2 Family P06839_71-257 1.3e-47 1 CL0023 Y 71 257   
ResIII Family Q00578_359-519 2.5e-16 1 CL0023 Z 359 519 m  H-Bb 
RNA_pol_Rpb1_R Repeat P04050_1676-1689 0.00091 1 No_clan k 11 24   
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
5sva.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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