3S16E

Rna polymerase ii initiation complex with an 8-nt rna
Total Genus 59
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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
59
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 59
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 3s16E01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3s16E02
4BBRE 1TWFE 2E2HE 5C4JE 2JA8E 3GTKE 2NVXE 4A3IE 3M4OE 3S1ME 4BBSE 4C3HE 1TWAE 3GTME 5IP7E 3HOUE 3HOYE 4A3LE 3PO2E 3S14E 3HKZH 3GTGE 3GTJE 4AYBH 4X6AE 3S15E 1EIKA 3S17E 5IYDE 5IP9E 4A93E 3GTOE 4A3EE 1K83E 4A3FE 5M5XE 3GTQE 3K7AE 4A3ME 3HOWE 3S2HE 2VUME 4QIWH 2JA7E 3S1NE 3HOZE 5C44E 2NVQE 3M3YE 2R93E 4A3BE 4BY7E 2WB1H 2E2JE 1Y1VE 2JA6E 1I6HE 4C3IE 5M5WE 3H3VF 2NVTE 4A3JE 1SFOE 1I3QE 2WAQH 5IYCE 1TWGE 4A3CE 5IYBE 2NVYE 1R9TE 3S2DE 3H0GE 5FLME 2JA5E 3RZDE 3S16E 3HOVE 3GTPE 2YU9E 4BXXE 1DZFA 3S1QE 3S1RE 2R7ZE 1Y1WE 5C4XE 4Y7NE 5M5YE 3PO3E 4A3DE 3CQZE 5FJ8E 3HOXE 1WCME 2Y0SH 4C2ME 1TWHE 4C3JE 2PMZH 3I4NE 3I4ME 5C3EE 5M3ME 2R92E 1TWCE 4Y52E 3GTLE 3RZOE 5M3FE 2B63E 1I50E 4A3GE 3FKIE 4BY1E 2E2IE 4A3KE
chains in the Genus database with same CATH superfamily
4BBRE 1TWFE 4GZYE 1TWGF 2E2HE 5C4JE 4OIPE 3S15F 5IYBF 2JA8E 3GTKE 3I4MF 3S17F 5IP9F 4A93F 4A3JF 4MEYE 3S2DF 2NVXE 4A3IE 2R92F 4A3EF 4QIWK 4XLPE 3M4OE 3S1ME 4BBSE 4C3HE 2YU9F 1TWAE 4BXXF 3GTLF 3RZOF 3GTME 5IP7E 2B63F 3HOUE 2O5IE 3HOYE 4A3LE 2JA7F 5IPLE 3PO2E 4A3CF 4Y7NF 5M5YF 3S14E 3HKZH 3GTGE 3GTJE 4AYBH 3M3YF 1ZYRE 2A69E 4X6AE 3S15E 5C4JF 1EIKA 5FLMF 5FJ8F 5D4DE 3S17E 5IYDE 5IP9E 4A93E 3GTPF 3HOVF 3GTOE 4A3IF 1I6HF 4A3EE 4KN4E 4YFKE 1K83E 4A3FE 4XSZE 4LK1E 4YG2E 4C3IF 5M5WF 4BBSF 5M5XE 3DXJE 3GTQE 3K7AE 4A3ME 2A6HE 4YFXE 3HOWE 2Y0SI 5C3EF 3S2HE 1HQME 5C4XF 1I3QF 4XLNE 2VUME 4QIWH 2JA7E 1TWCF 3S1NE 4Y52F 3HOZE 3S14F 5C44E 2NVQE 3M3YE 2R93E 3GTJF 4G7ZE 5D4CE 4A3BE 4BY7E 4X6AF 2WB1H 1I50F 2E2JE 5IYDF 5BYHE 1Y1VE 2JA6E 2PMZK 4LLGE 2NVYF 1I6HE 4A3KF 2E2IF 1R9TF 3I4NF 4BBRF 4LJZE 5M3MF 4C3IE 5M5WE 3H3VG 4A3MF 2JA5F 3H3VF 2NVTE 4A3JE 4G7HE 2WB1I 5E17E 1SFOE 1I3QE 2WAQH 4Q5SE 3EQLE 5M3FF 3S1QF 4JK1E 5D4EE 4A3GF 1TWAF 5IYCE 5C44F 1Y1WF 2NVQF 2R93F 3FKIF 3WODE 4BY1F 2A6EE 5IP7F 4OIRE 1YNJK 4BY7F 4A3BF 3PO3F 3HOUF 1TWFF 1TWGE 4Q4ZE 2E2JF 5TMFE 4A3CE 5IYBE 3PO2F 2JA8F 3GTKF 2NVYE 3HOXF 1R9TE 3S2DE 4C2MF 3H0GE 5FLME 1IW7E 2JA5E 1TWHF 4C3JF 3RZDE 3S16E 4C3HF 3HOVE 3GTPE 2NVTF 2YU9E 4BXXE 1DZFA 4KN7E 1SFOF 3GTOF 1K83F 3GTMF 1I6VE 2A68E 1QKLA 4A3FF 3S1QE 2WAQK 3S1RE 4ZH4E 3GTQF 3HOYF 2BE5E 2R7ZE 1Y1WE 4MQ9E 5IYCF 4A3LF 5C4XE 2PPBE 3HOWF 4Y7NE 5M5YE 4G7OE 3PO3E 4A3DE 1YNNK 2KRXA 4MEXE 2VUMF 3CQZE 3S1NF 5FJ8E 3HOXE 1WCME 2Y0SH 2CW0E 4C2ME 3H0GF 1SMYE 4AYBK 1TWHE 4C3JE 3RZDF 2E2HF 2PMZH 5M5XF 1Y1VF 3S16F 3I4NE 3K7AF 3I4ME 4XSXE 4OIQE 4LK0E 5C3EE 5M3ME 3S2HF 2R92E 2NVXF 3S1RF 3M4OF 2R7ZF 3S1MF 1TWCE 4Y52E 3HOZF 4YFNE 3GTLE 4A3DF 3RZOE 4KMUE 2JA6F 5E18E 5M3FE 2B63E 3CQZF 4OIOE 2O5JE 1I50E 4A3GE 4OINE 3HKZK 1WCMF 5TMCE 3FKIE 4BY1E 2E2IE 4A3KE 3GTGF
chains in the Genus database with same CATH topology
4BBRE 1TWFE 2E2HE 5C4JE 2JA8E 3GTKE 2NVXE 4A3IE 3M4OE 3S1ME 4BBSE 4C3HE 1TWAE 3GTME 5IP7E 3HOUE 3HOYE 4A3LE 3PO2E 3S14E 3HKZH 3GTGE 3GTJE 4AYBH 4X6AE 3S15E 1EIKA 3S17E 5IYDE 5IP9E 4A93E 3GTOE 4A3EE 1K83E 4A3FE 5M5XE 3GTQE 3K7AE 4A3ME 3HOWE 3S2HE 2VUME 4QIWH 2JA7E 3S1NE 3HOZE 5C44E 2NVQE 3M3YE 2R93E 4A3BE 4BY7E 2WB1H 2E2JE 1Y1VE 2JA6E 1I6HE 4C3IE 5M5WE 3H3VF 2NVTE 4A3JE 1SFOE 1I3QE 2WAQH 5IYCE 1TWGE 4A3CE 5IYBE 2NVYE 1R9TE 3S2DE 3H0GE 5FLME 2JA5E 3RZDE 3S16E 3HOVE 3GTPE 2YU9E 4BXXE 1DZFA 3S1QE 3S1RE 2R7ZE 1Y1WE 5C4XE 4Y7NE 5M5YE 3PO3E 4A3DE 3CQZE 5FJ8E 3HOXE 1WCME 2Y0SH 4C2ME 1TWHE 4C3JE 2PMZH 3I4NE 3I4ME 5C3EE 5M3ME 2R92E 1TWCE 4Y52E 3GTLE 3RZOE 5M3FE 2B63E 1I50E 4A3GE 3FKIE 4BY1E 2E2IE 4A3KE
chains in the Genus database with same CATH homology


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