3S1ME

Rna polymerase ii initiation complex with a 5-nt rna (variant 1)
Total Genus 64
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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
64
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 64
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-05-15

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 3s1mE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3s1mE02
5C3EE 4C3IE 1TWCE 3GTJE 5M3FE 3CQZE 3RZDE 4BBRE 4AYBH 3GTOE 2E2JE 4A3ME 1I6HE 1TWAE 1TWFE 5IYCE 5IP9E 4C2ME 2NVQE 1K83E 3M4OE 5IP7E 4BBSE 3GTKE 2NVTE 3S2HE 4A3FE 3GTQE 5IYDE 4Y7NE 3S15E 4A3LE 5IYBE 3I4NE 3S17E 3FKIE 2JA7E 4BXXE 1TWGE 3S1ME 1EIKA 3HOUE 3S2DE 2VUME 5M5WE 1TWHE 3GTGE 3H3VF 3S1QE 3PO3E 5FJ8E 2NVYE 3HOZE 3I4ME 1SFOE 2E2HE 3GTLE 4A3GE 2PMZH 5C44E 3S1NE 4A3DE 2WAQH 5M5XE 3PO2E 4Y52E 3H0GE 1Y1WE 3M3YE 2NVXE 3S16E 1DZFA 3HOVE 5C4JE 1R9TE 2R7ZE 4A3JE 2JA6E 3HOXE 1Y1VE 5M3ME 1WCME 3HOYE 4A3EE 4A3BE 2JA8E 3RZOE 4QIWH 5M5YE 3GTME 2YU9E 2Y0SH 3S14E 4C3JE 1I3QE 3S1RE 4BY1E 4BY7E 4X6AE 3HOWE 2JA5E 4A93E 2B63E 4A3KE 3K7AE 4C3HE 2E2IE 5FLME 1I50E 4A3IE 2WB1H 3GTPE 3HKZH 2R93E 5C4XE 4A3CE 2R92E
chains in the Genus database with same CATH superfamily
5C44F 5C3EE 4C3IE 4XSZE 2B63F 1TWCE 5E17E 1R9TF 5IYBF 3GTJE 5M3FE 3CQZE 3PO3F 3S17F 3RZDE 3GTOF 4A3MF 5FJ8F 2YU9F 4BBRE 4LLGE 4Y52F 4AYBH 2NVXF 3GTOE 2O5IE 3CQZF 5BYHE 4BBRF 2E2JE 4A3ME 1I6HE 1K83F 4LK1E 5C4JF 2NVQF 1TWAE 2E2JF 4ZH4E 3I4MF 1I3QF 5D4DE 3S1RF 4LJZE 3S16F 4A3BF 3HOYF 4AYBK 4YFNE 1TWFE 2JA6F 5M5YF 5IYCE 5IP9E 2A69E 4A3DF 4C2ME 5IP7F 2A6HE 2BE5E 2NVQE 1K83E 3M4OE 1TWGF 2E2HF 4MEYE 4G7OE 2JA5F 5IP7E 3HOVF 4BBSE 3GTKE 2NVTE 3S2HE 1TWHF 4A3FE 3GTMF 3S1QF 3GTQE 5IYDE 4Y7NE 4A3IF 2E2IF 2R7ZF 3H0GF 3GTKF 3S15E 4A3LE 4OINE 5IYBE 3I4NE 3S1MF 3S2HF 3S17E 3EQLE 4YFKE 3HOWF 3FKIE 2JA7E 4BXXE 1SMYE 3I4NF 1TWGE 4G7ZE 3S1ME 2PMZK 3S15F 4A3LF 4Q5SE 4A3CF 1EIKA 3HOUE 3S2DE 1WCMF 4KN7E 4XLNE 2VUME 3S14F 5M5WE 1TWHE 3GTGE 3H3VF 2A68E 2WAQK 3S1QE 4A3FF 3PO3E 2Y0SI 5FJ8E 2NVYE 3HOZE 2VUMF 3I4ME 1SFOE 2E2HE 3M4OF 3GTLE 4A3GE 2PMZH 4A3KF 5C4XF 3K7AF 5C44E 3FKIF 4OIOE 2R92F 2A6EE 4A3EF 1I6HF 2NVYF 3HOZF 2KRXA 3S1NE 4A3DE 1SFOF 2WAQH 5M5XE 3PO2E 3GTQF 3HOXF 5TMCE 4Y52E 4Q4ZE 3H0GE 1Y1WE 3M3YE 1YNNK 2NVXE 5D4EE 4YG2E 3S16E 2O5JE 2CW0E 1DZFA 5FLMF 3HOVE 5TMFE 5M5XF 4A3JF 1TWCF 3PO2F 5IPLE 4YFXE 5C3EF 5C4JE 4G7HE 1R9TE 1I6VE 4KN4E 1IW7E 4XSXE 2R7ZE 4MEXE 4A3JE 2JA6E 3HOXE 4GZYE 4MQ9E 2NVTF 5IP9F 5IYCF 1YNJK 1Y1WF 3M3YF 3GTJF 1Y1VE 5M3ME 3DXJE 5M3FF 3RZOF 3RZDF 1WCME 3HOYE 4A3EE 4A3BE 4A93F 2JA8E 3RZOE 4QIWH 5M5YE 4C3JF 4BY7F 4OIQE 3GTPF 3GTME 5E18E 5D4CE 2YU9E 2Y0SH 3HOUF 3S14E 4C3JE 1I3QE 3S1RE 4LK0E 3H3VG 3S2DF 3HKZK 3S1NF 4BY1E 4BY7E 4X6AE 4C3HF 3HOWE 2JA5E 4QIWK 4A93E 2B63E 2JA7F 4A3KE 4BY1F 3GTLF 4BXXF 4XLPE 4A3GF 3K7AE 4C3HE 4C2MF 4X6AF 4OIPE 2E2IE 4Y7NF 5FLME 5IYDF 2R93F 2WB1I 4KMUE 1QKLA 1I50E 4A3IE 2WB1H 3GTPE 1Y1VF 3HKZH 5M3MF 5M5WF 2PPBE 3GTGF 1HQME 2R93E 4BBSF 1TWFF 3WODE 1ZYRE 1I50F 4C3IF 4JK1E 5C4XE 2JA8F 1TWAF 4A3CE 2R92E 4OIRE
chains in the Genus database with same CATH topology
5C3EE 4C3IE 1TWCE 3GTJE 5M3FE 3CQZE 3RZDE 4BBRE 4AYBH 3GTOE 2E2JE 4A3ME 1I6HE 1TWAE 1TWFE 5IYCE 5IP9E 4C2ME 2NVQE 1K83E 3M4OE 5IP7E 4BBSE 3GTKE 2NVTE 3S2HE 4A3FE 3GTQE 5IYDE 4Y7NE 3S15E 4A3LE 5IYBE 3I4NE 3S17E 3FKIE 2JA7E 4BXXE 1TWGE 3S1ME 1EIKA 3HOUE 3S2DE 2VUME 5M5WE 1TWHE 3GTGE 3H3VF 3S1QE 3PO3E 5FJ8E 2NVYE 3HOZE 3I4ME 1SFOE 2E2HE 3GTLE 4A3GE 2PMZH 5C44E 3S1NE 4A3DE 2WAQH 5M5XE 3PO2E 4Y52E 3H0GE 1Y1WE 3M3YE 2NVXE 3S16E 1DZFA 3HOVE 5C4JE 1R9TE 2R7ZE 4A3JE 2JA6E 3HOXE 1Y1VE 5M3ME 1WCME 3HOYE 4A3EE 4A3BE 2JA8E 3RZOE 4QIWH 5M5YE 3GTME 2YU9E 2Y0SH 3S14E 4C3JE 1I3QE 3S1RE 4BY1E 4BY7E 4X6AE 3HOWE 2JA5E 4A93E 2B63E 4A3KE 3K7AE 4C3HE 2E2IE 5FLME 1I50E 4A3IE 2WB1H 3GTPE 3HKZH 2R93E 5C4XE 4A3CE 2R92E
chains in the Genus database with same CATH homology


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