3S17E

Rna polymerase ii initiation complex with a 9-nt rna
Total Genus 56
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
56
sequence length
214
structure length
214
Chain Sequence
DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 56
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-05-14

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E PF01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain
E PF03871 RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 RNA polymerase, Rpb5, N-terminal domain 3s17E01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3s17E02
2E2HE 4C3HE 2JA7E 1WCME 1TWHE 1TWGE 1TWFE 2JA5E 3RZDE 2E2JE 3S15E 4C3JE 3S17E 5C4XE 1I6HE 3GTQE 3I4NE 2NVXE 4A3ME 2JA6E 4A3DE 1R9TE 4A3CE 2R92E 3H3VF 3GTKE 4A93E 2R7ZE 3S16E 1K83E 5M3ME 3M4OE 5C3EE 3S2HE 3HOVE 1SFOE 4BY1E 3HOYE 3HOZE 4A3JE 1DZFA 2WB1H 5IYBE 3S2DE 4C3IE 2WAQH 4Y52E 4Y7NE 5M3FE 2B63E 3S1NE 2VUME 3GTPE 2NVTE 3PO3E 4A3BE 2JA8E 3GTJE 2E2IE 3GTME 1TWAE 5IP9E 3GTOE 1TWCE 4BY7E 3GTLE 1I50E 4A3IE 5IYDE 5C4JE 2R93E 4X6AE 5FLME 2Y0SH 3S1QE 5IYCE 3CQZE 2YU9E 2NVQE 5M5WE 3K7AE 1Y1WE 4BXXE 3H0GE 4A3GE 5FJ8E 4BBSE 4A3EE 3HKZH 5IP7E 3S1ME 5M5YE 3HOWE 3M3YE 2NVYE 3RZOE 4AYBH 5C44E 4A3KE 3I4ME 1I3QE 4BBRE 3FKIE 1Y1VE 3HOUE 3GTGE 5M5XE 3S1RE 3S14E 4C2ME 4A3LE 4QIWH 2PMZH 3HOXE 3PO2E 1EIKA 4A3FE
chains in the Genus database with same CATH superfamily
1WCMF 2A68E 2E2HE 4C3HE 2JA7E 3HKZK 4JK1E 4C3HF 3HOVF 1WCME 3HOXF 2O5JE 1TWHE 4BXXF 1TWGE 5M5WF 1Y1WF 4LK0E 5E17E 2R92F 3GTGF 1TWFE 2JA5E 3S1QF 3RZDE 2E2JE 4LJZE 4BBRF 4A3DF 3S15E 4C3JE 3S17E 5C4XE 1I6VE 1I6HE 3GTQE 1QKLA 3I4NE 2NVXF 3EQLE 3RZOF 2NVYF 4BY1F 3M3YF 2NVXE 4A3ME 5C4XF 2JA6E 3S17F 4A3DE 3S15F 2A69E 5M5YF 4YFNE 5C3EF 4BY7F 1R9TE 4A3CE 1K83F 5M3MF 3GTOF 1TWFF 3S16F 2R92E 5FJ8F 2Y0SI 3GTMF 4LK1E 3H3VF 1IW7E 3GTKE 4A93F 4A93E 4MEYE 4XSZE 4A3BF 2YU9F 2R7ZE 3CQZF 3S16E 2A6EE 4OIRE 1K83E 5M3ME 3M4OE 4A3CF 1R9TF 5C3EE 4XLPE 2B63F 3S2HE 3HOVE 4LLGE 3H3VG 2JA7F 1SFOE 4Y7NF 4GZYE 4G7HE 4BY1E 3HOYE 3PO2F 3HOZE 5C4JF 4A3IF 4A3JE 4OIOE 4C3IF 3S14F 1YNJK 3GTLF 3S1RF 5M5XF 3HOWF 1DZFA 2E2JF 4QIWK 3RZDF 1ZYRE 2WB1H 5BYHE 5IYBE 1TWAF 1I3QF 2E2IF 3S2DE 3I4MF 4C3IE 1TWHF 4A3JF 2WAQH 2NVTF 4Y52E 4Y7NE 1SFOF 3S1MF 4G7OE 5D4CE 5IP7F 4OIQE 5M3FE 2B63E 3S1NE 2WAQK 1SMYE 3M4OF 2VUME 4YFKE 3GTPE 2NVTE 3PO3E 4A3BE 2JA8E 2PMZK 3GTKF 4C2MF 3GTJE 3K7AF 2E2IE 4A3LF 3GTME 1TWAE 5IP9E 3GTOE 1HQME 3HOUF 1Y1VF 1TWCE 4BY7E 3FKIF 4YFXE 5TMCE 3GTLE 4Q4ZE 3WODE 5FLMF 1I50E 4X6AF 4A3MF 4MEXE 1YNNK 4A3IE 5IYDE 2R93F 2PPBE 5C4JE 3HOZF 4KN4E 2R93E 4AYBK 3GTQF 2BE5E 1I6HF 4X6AE 4KMUE 5FLME 3S2HF 2Y0SH 2WB1I 4A3EF 4BBSF 3S1QE 5D4EE 5IYCE 2JA5F 3CQZE 2YU9E 4XSXE 2R7ZF 4Q5SE 4XLNE 2NVQE 5M5WE 3K7AE 1Y1WE 4BXXE 1TWGF 3H0GE 4A3GE 3H0GF 4ZH4E 3GTJF 2NVQF 5FJ8E 4KN7E 3PO3F 3GTPF 5IYCF 2VUMF 4BBSE 4MQ9E 4YG2E 4A3EE 3HKZH 5M3FF 5IP7E 2JA6F 3S1ME 2E2HF 5M5YE 2KRXA 4Y52F 4A3FF 3HOWE 3M3YE 2NVYE 3RZOE 5IYDF 4AYBH 4OINE 3I4NF 5C44E 4A3KE 4A3GF 1I50F 4C3JF 3I4ME 3S2DF 1I3QE 4BBRE 5IYBF 3FKIE 1Y1VE 1TWCF 3HOUE 5IP9F 3GTGE 5M5XE 4G7ZE 3S1RE 3S14E 4C2ME 4A3LE 2A6HE 4QIWH 4OIPE 2JA8F 4A3KF 3DXJE 5C44F 5TMFE 5D4DE 2PMZH 2CW0E 2O5IE 3HOXE 3PO2E 3HOYF 5IPLE 5E18E 1EIKA 3S1NF 4A3FE
chains in the Genus database with same CATH topology
2E2HE 4C3HE 2JA7E 1WCME 1TWHE 1TWGE 1TWFE 2JA5E 3RZDE 2E2JE 3S15E 4C3JE 3S17E 5C4XE 1I6HE 3GTQE 3I4NE 2NVXE 4A3ME 2JA6E 4A3DE 1R9TE 4A3CE 2R92E 3H3VF 3GTKE 4A93E 2R7ZE 3S16E 1K83E 5M3ME 3M4OE 5C3EE 3S2HE 3HOVE 1SFOE 4BY1E 3HOYE 3HOZE 4A3JE 1DZFA 2WB1H 5IYBE 3S2DE 4C3IE 2WAQH 4Y52E 4Y7NE 5M3FE 2B63E 3S1NE 2VUME 3GTPE 2NVTE 3PO3E 4A3BE 2JA8E 3GTJE 2E2IE 3GTME 1TWAE 5IP9E 3GTOE 1TWCE 4BY7E 3GTLE 1I50E 4A3IE 5IYDE 5C4JE 2R93E 4X6AE 5FLME 2Y0SH 3S1QE 5IYCE 3CQZE 2YU9E 2NVQE 5M5WE 3K7AE 1Y1WE 4BXXE 3H0GE 4A3GE 5FJ8E 4BBSE 4A3EE 3HKZH 5IP7E 3S1ME 5M5YE 3HOWE 3M3YE 2NVYE 3RZOE 4AYBH 5C44E 4A3KE 3I4ME 1I3QE 4BBRE 3FKIE 1Y1VE 3HOUE 3GTGE 5M5XE 3S1RE 3S14E 4C2ME 4A3LE 4QIWH 2PMZH 3HOXE 3PO2E 1EIKA 4A3FE
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2E2H E;  4C3H E;  2JA7 E;  1WCM E;  1TWH E;  1TWG E;  1TWF E;  2JA5 E;  3RZD E;  2E2J E;  3S15 E;  4C3J E;  3S17 E;  5C4X E;  1I6H E;  3GTQ E;  3I4N E;  2NVX E;  4A3M E;  2JA6 E;  4A3D E;  1R9T E;  4A3C E;  2R92 E;  3H3V F;  3GTK E;  4A93 E;  2R7Z E;  3S16 E;  1K83 E;  5M3M E;  3M4O E;  5C3E E;  3S2H E;  3HOV E;  1SFO E;  4BY1 E;  3HOY E;  3HOZ E;  4A3J E;  1DZF A;  2WB1 H;  5IYB E;  3S2D E;  4C3I E;  2WAQ H;  4Y52 E;  4Y7N E;  5M3F E;  2B63 E;  3S1N E;  2VUM E;  3GTP E;  2NVT E;  3PO3 E;  4A3B E;  2JA8 E;  3GTJ E;  2E2I E;  3GTM E;  1TWA E;  5IP9 E;  3GTO E;  1TWC E;  4BY7 E;  3GTL E;  1I50 E;  4A3I E;  5IYD E;  5C4J E;  2R93 E;  4X6A E;  5FLM E;  2Y0S H;  3S1Q E;  5IYC E;  3CQZ E;  2YU9 E;  2NVQ E;  5M5W E;  3K7A E;  1Y1W E;  4BXX E;  3H0G E;  4A3G E;  5FJ8 E;  4BBS E;  4A3E E;  3HKZ H;  5IP7 E;  3S1M E;  5M5Y E;  3HOW E;  3M3Y E;  2NVY E;  3RZO E;  4AYB H;  5C44 E;  4A3K E;  3I4M E;  1I3Q E;  4BBR E;  3FKI E;  1Y1V E;  3HOU E;  3GTG E;  5M5X E;  3S1R E;  3S14 E;  4C2M E;  4A3L E;  4QIW H;  2PMZ H;  3HOX E;  3PO2 E;  1EIK A;  4A3F E; 
#chains in the Genus database with same CATH topology
 1WCM F;  2A68 E;  2E2H E;  4C3H E;  2JA7 E;  3HKZ K;  4JK1 E;  4C3H F;  3HOV F;  1WCM E;  3HOX F;  2O5J E;  1TWH E;  4BXX F;  1TWG E;  5M5W F;  1Y1W F;  4LK0 E;  5E17 E;  2R92 F;  3GTG F;  1TWF E;  2JA5 E;  3S1Q F;  3RZD E;  2E2J E;  4LJZ E;  4BBR F;  4A3D F;  3S15 E;  4C3J E;  3S17 E;  5C4X E;  1I6V E;  1I6H E;  3GTQ E;  1QKL A;  3I4N E;  2NVX F;  3EQL E;  3RZO F;  2NVY F;  4BY1 F;  3M3Y F;  2NVX E;  4A3M E;  5C4X F;  2JA6 E;  3S17 F;  4A3D E;  3S15 F;  2A69 E;  5M5Y F;  4YFN E;  5C3E F;  4BY7 F;  1R9T E;  4A3C E;  1K83 F;  5M3M F;  3GTO F;  1TWF F;  3S16 F;  2R92 E;  5FJ8 F;  2Y0S I;  3GTM F;  4LK1 E;  3H3V F;  1IW7 E;  3GTK E;  4A93 F;  4A93 E;  4MEY E;  4XSZ E;  4A3B F;  2YU9 F;  2R7Z E;  3CQZ F;  3S16 E;  2A6E E;  4OIR E;  1K83 E;  5M3M E;  3M4O E;  4A3C F;  1R9T F;  5C3E E;  4XLP E;  2B63 F;  3S2H E;  3HOV E;  4LLG E;  3H3V G;  2JA7 F;  1SFO E;  4Y7N F;  4GZY E;  4G7H E;  4BY1 E;  3HOY E;  3PO2 F;  3HOZ E;  5C4J F;  4A3I F;  4A3J E;  4OIO E;  4C3I F;  3S14 F;  1YNJ K;  3GTL F;  3S1R F;  5M5X F;  3HOW F;  1DZF A;  2E2J F;  4QIW K;  3RZD F;  1ZYR E;  2WB1 H;  5BYH E;  5IYB E;  1TWA F;  1I3Q F;  2E2I F;  3S2D E;  3I4M F;  4C3I E;  1TWH F;  4A3J F;  2WAQ H;  2NVT F;  4Y52 E;  4Y7N E;  1SFO F;  3S1M F;  4G7O E;  5D4C E;  5IP7 F;  4OIQ E;  5M3F E;  2B63 E;  3S1N E;  2WAQ K;  1SMY E;  3M4O F;  2VUM E;  4YFK E;  3GTP E;  2NVT E;  3PO3 E;  4A3B E;  2JA8 E;  2PMZ K;  3GTK F;  4C2M F;  3GTJ E;  3K7A F;  2E2I E;  4A3L F;  3GTM E;  1TWA E;  5IP9 E;  3GTO E;  1HQM E;  3HOU F;  1Y1V F;  1TWC E;  4BY7 E;  3FKI F;  4YFX E;  5TMC E;  3GTL E;  4Q4Z E;  3WOD E;  5FLM F;  1I50 E;  4X6A F;  4A3M F;  4MEX E;  1YNN K;  4A3I E;  5IYD E;  2R93 F;  2PPB E;  5C4J E;  3HOZ F;  4KN4 E;  2R93 E;  4AYB K;  3GTQ F;  2BE5 E;  1I6H F;  4X6A E;  4KMU E;  5FLM E;  3S2H F;  2Y0S H;  2WB1 I;  4A3E F;  4BBS F;  3S1Q E;  5D4E E;  5IYC E;  2JA5 F;  3CQZ E;  2YU9 E;  4XSX E;  2R7Z F;  4Q5S E;  4XLN E;  2NVQ E;  5M5W E;  3K7A E;  1Y1W E;  4BXX E;  1TWG F;  3H0G E;  4A3G E;  3H0G F;  4ZH4 E;  3GTJ F;  2NVQ F;  5FJ8 E;  4KN7 E;  3PO3 F;  3GTP F;  5IYC F;  2VUM F;  4BBS E;  4MQ9 E;  4YG2 E;  4A3E E;  3HKZ H;  5M3F F;  5IP7 E;  2JA6 F;  3S1M E;  2E2H F;  5M5Y E;  2KRX A;  4Y52 F;  4A3F F;  3HOW E;  3M3Y E;  2NVY E;  3RZO E;  5IYD F;  4AYB H;  4OIN E;  3I4N F;  5C44 E;  4A3K E;  4A3G F;  1I50 F;  4C3J F;  3I4M E;  3S2D F;  1I3Q E;  4BBR E;  5IYB F;  3FKI E;  1Y1V E;  1TWC F;  3HOU E;  5IP9 F;  3GTG E;  5M5X E;  4G7Z E;  3S1R E;  3S14 E;  4C2M E;  4A3L E;  2A6H E;  4QIW H;  4OIP E;  2JA8 F;  4A3K F;  3DXJ E;  5C44 F;  5TMF E;  5D4D E;  2PMZ H;  2CW0 E;  2O5I E;  3HOX E;  3PO2 E;  3HOY F;  5IPL E;  5E18 E;  1EIK A;  3S1N F;  4A3F E; 
#chains in the Genus database with same CATH homology
 2E2H E;  4C3H E;  2JA7 E;  1WCM E;  1TWH E;  1TWG E;  1TWF E;  2JA5 E;  3RZD E;  2E2J E;  3S15 E;  4C3J E;  3S17 E;  5C4X E;  1I6H E;  3GTQ E;  3I4N E;  2NVX E;  4A3M E;  2JA6 E;  4A3D E;  1R9T E;  4A3C E;  2R92 E;  3H3V F;  3GTK E;  4A93 E;  2R7Z E;  3S16 E;  1K83 E;  5M3M E;  3M4O E;  5C3E E;  3S2H E;  3HOV E;  1SFO E;  4BY1 E;  3HOY E;  3HOZ E;  4A3J E;  1DZF A;  2WB1 H;  5IYB E;  3S2D E;  4C3I E;  2WAQ H;  4Y52 E;  4Y7N E;  5M3F E;  2B63 E;  3S1N E;  2VUM E;  3GTP E;  2NVT E;  3PO3 E;  4A3B E;  2JA8 E;  3GTJ E;  2E2I E;  3GTM E;  1TWA E;  5IP9 E;  3GTO E;  1TWC E;  4BY7 E;  3GTL E;  1I50 E;  4A3I E;  5IYD E;  5C4J E;  2R93 E;  4X6A E;  5FLM E;  2Y0S H;  3S1Q E;  5IYC E;  3CQZ E;  2YU9 E;  2NVQ E;  5M5W E;  3K7A E;  1Y1W E;  4BXX E;  3H0G E;  4A3G E;  5FJ8 E;  4BBS E;  4A3E E;  3HKZ H;  5IP7 E;  3S1M E;  5M5Y E;  3HOW E;  3M3Y E;  2NVY E;  3RZO E;  4AYB H;  5C44 E;  4A3K E;  3I4M E;  1I3Q E;  4BBR E;  3FKI E;  1Y1V E;  3HOU E;  3GTG E;  5M5X E;  3S1R E;  3S14 E;  4C2M E;  4A3L E;  4QIW H;  2PMZ H;  3HOX E;  3PO2 E;  1EIK A;  4A3F E; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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