1WCME

Complete 12-subunit rna polymerase ii at 3.8 angstrom
Total Genus 48
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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
48
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 Structures of Complete RNA Polymerase II and its Subcomplex,Rpb4/7
pubmed doi rcsb
molecule tags Transcription
source organism Saccharomyces cerevisiae
molecule keywords DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
total genus 48
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2004-11-17

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 1wcmE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 1wcmE02
5C4XE 5M3ME 2WAQH 2JA6E 2R93E 2JA5E 1TWFE 1Y1WE 2YU9E 4Y7NE 3HOYE 2JA8E 1SFOE 3GTQE 5IP7E 4BY1E 3HOWE 3RZOE 3GTJE 3S1RE 5FLME 5C3EE 4C3IE 2VUME 4C3JE 5IP9E 4QIWH 5M5XE 3GTLE 3S1QE 1K83E 3HOVE 4A3KE 3S2HE 3I4ME 3M3YE 1R9TE 3HOUE 3K7AE 3PO3E 1I3QE 5C4JE 5IYCE 1DZFA 1Y1VE 5M5YE 4AYBH 2NVTE 3S14E 3S2DE 4A3IE 3FKIE 4A3CE 4A3BE 2NVXE 3GTGE 4BXXE 1I6HE 1TWGE 2NVQE 3HOXE 3RZDE 3I4NE 1EIKA 2E2JE 3S1NE 5M3FE 1TWCE 3HKZH 5IYDE 3GTKE 3GTME 4A3JE 3PO2E 2E2IE 1TWHE 1TWAE 3S16E 4A3GE 2E2HE 5M5WE 1I50E 1WCME 4A3LE 2Y0SH 2JA7E 4X6AE 3H3VF 2WB1H 3GTOE 5FJ8E 4BY7E 3HOZE 2R92E 4BBRE 4C2ME 4A3EE 2NVYE 3CQZE 2B63E 4C3HE 5IYBE 5C44E 2R7ZE 4Y52E 2PMZH 3S15E 3S1ME 3H0GE 3S17E 3M4OE 4A93E 4A3FE 4A3ME 4A3DE 3GTPE 4BBSE
chains in the Genus database with same CATH superfamily
5C4XE 5M3ME 3I4MF 4MEYE 3M3YF 3HKZK 2WAQH 1R9TF 2JA6E 1I6VE 3K7AF 3HOUF 3HOYF 4G7OE 2R93E 2JA5E 1TWFE 1Y1WE 2YU9E 4Y7NE 3GTQF 1I3QF 4JK1E 5C4JF 4XSXE 5D4EE 4OIQE 4Q5SE 3WODE 3HOYE 5IYCF 2JA8E 5M5YF 1Y1VF 1SFOE 3GTQE 5IP7E 4BY1E 4A3KF 2NVTF 4LLGE 3HOWE 4A3IF 3S2DF 3FKIF 4XLNE 2A68E 4A3CF 3RZOE 4XSZE 2Y0SI 4MEXE 3EQLE 3GTJE 2NVXF 4A3BF 3S1RE 5FLME 5C3EE 4C3IE 4KN7E 3S1QF 3GTGF 2VUME 4BXXF 4GZYE 4C3JE 1I6HF 5IP9E 4QIWH 5M5XE 1TWGF 2NVQF 4KMUE 3HOXF 4OIPE 3RZDF 3GTLE 2E2JF 3S1QE 3S1NF 4KN4E 2PPBE 1K83E 3HOVE 1TWCF 4YFXE 5IYDF 2PMZK 4A3KE 3GTKF 3S2HE 4A3JF 3PO3F 3PO2F 2E2IF 1TWHF 4YG2E 4YFNE 4OINE 3I4ME 3M3YE 1TWAF 3S16F 1R9TE 3HOUE 3K7AE 4OIOE 5M5WF 4A3GF 5TMCE 5E18E 3PO3E 1I50F 5D4CE 1I3QE 3S14F 5C4JE 2JA7F 3S2HF 4LK0E 2WAQK 5D4DE 3GTOF 2KRXA 5TMFE 5FJ8F 5IYCE 4BY7F 1DZFA 1Y1VE 5M5YE 4Q4ZE 3HOZF 2A69E 2A6HE 4AYBH 2NVTE 2WB1I 3S14E 3S2DE 4A3IE 4BBRF 2R92F 3H3VG 4C2MF 3FKIE 4A3CE 4A3BE 2NVXE 4A3EF 3I4NF 2NVYF 2BE5E 3CQZF 3GTGE 4BXXE 2CW0E 2B63F 5M3FF 1I6HE 4C3HF 5IYBF 5C44F 4Y52F 1TWGE 2O5IE 3S1MF 2NVQE 3S15F 5IPLE 3HOXE 3GTMF 3S17F 3RZDE 3M4OF 3I4NE 1EIKA 2E2JE 3S1NE 4A3FF 5M3FE 1TWCE 4MQ9E 3HKZH 4A3MF 5IYDE 4QIWK 4ZH4E 2E2HF 4A3DF 3GTPF 4YFKE 3GTKE 4BBSF 4X6AF 3GTME 4A3JE 1WCMF 4A3LF 4G7ZE 3PO2E 2E2IE 1TWHE 5M3MF 5C4XF 2A6EE 1YNJK 1TWAE 3S16E 1ZYRE 5BYHE 4A3GE 2JA6F 2E2HE 5M5WE 5E17E 4OIRE 2R93F 1I50E 1YNNK 1TWFF 1WCME 4A3LE 4Y7NF 1Y1WF 2Y0SH 2JA5F 1SMYE 2YU9F 2JA7E 4X6AE 3H3VF 2WB1H 3GTOE 4LK1E 5FJ8E 4BY7E 2JA8F 1SFOF 3HOZE 1QKLA 4BY1F 5IP7F 2R92E 4LJZE 3HOWF 4BBRE 3DXJE 4C2ME 2R7ZF 3H0GF 3RZOF 3GTJF 3S1RF 4A3EE 5FLMF 5C3EF 4C3IF 2NVYE 3CQZE 4AYBK 4A93F 2VUMF 2B63E 2O5JE 4C3JF 4C3HE 5IYBE 5IP9F 5C44E 2R7ZE 4Y52E 1IW7E 2PMZH 3S15E 3S1ME 3H0GE 5M5XF 3S17E 4G7HE 3M4OE 3GTLF 4A93E 4A3FE 4A3ME 4A3DE 1K83F 3HOVF 3GTPE 4XLPE 4BBSE 1HQME
chains in the Genus database with same CATH topology
5C4XE 5M3ME 2WAQH 2JA6E 2R93E 2JA5E 1TWFE 1Y1WE 2YU9E 4Y7NE 3HOYE 2JA8E 1SFOE 3GTQE 5IP7E 4BY1E 3HOWE 3RZOE 3GTJE 3S1RE 5FLME 5C3EE 4C3IE 2VUME 4C3JE 5IP9E 4QIWH 5M5XE 3GTLE 3S1QE 1K83E 3HOVE 4A3KE 3S2HE 3I4ME 3M3YE 1R9TE 3HOUE 3K7AE 3PO3E 1I3QE 5C4JE 5IYCE 1DZFA 1Y1VE 5M5YE 4AYBH 2NVTE 3S14E 3S2DE 4A3IE 3FKIE 4A3CE 4A3BE 2NVXE 3GTGE 4BXXE 1I6HE 1TWGE 2NVQE 3HOXE 3RZDE 3I4NE 1EIKA 2E2JE 3S1NE 5M3FE 1TWCE 3HKZH 5IYDE 3GTKE 3GTME 4A3JE 3PO2E 2E2IE 1TWHE 1TWAE 3S16E 4A3GE 2E2HE 5M5WE 1I50E 1WCME 4A3LE 2Y0SH 2JA7E 4X6AE 3H3VF 2WB1H 3GTOE 5FJ8E 4BY7E 3HOZE 2R92E 4BBRE 4C2ME 4A3EE 2NVYE 3CQZE 2B63E 4C3HE 5IYBE 5C44E 2R7ZE 4Y52E 2PMZH 3S15E 3S1ME 3H0GE 3S17E 3M4OE 4A93E 4A3FE 4A3ME 4A3DE 3GTPE 4BBSE
chains in the Genus database with same CATH homology


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