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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molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
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
5C4XE 3S1RE 1WCME 3S2DE 2JA7E 2R93E 4AYBH 1TWAE 4A3CE 4A3FE 2VUME 3H3VF 1SFOE 5IP7E 2E2JE 4Y7NE 3I4NE 4C3HE 2B63E 3HOWE 4C2ME 5FJ8E 3S17E 5C4JE 4C3JE 4BBRE 4A3GE 5M3FE 3PO2E 4BXXE 4X6AE 5IYBE 2WAQH 1TWHE 2JA8E 3GTME 3S1QE 4BBSE 3S1ME 3HOXE 4A3IE 5FLME 2E2HE 4A3EE 1DZFA 3GTLE 2Y0SH 3GTPE 1TWCE 3HOUE 3HOZE 2NVXE 3HKZH 2YU9E 2JA5E 1R9TE 2NVTE 1I6HE 4C3IE 3RZOE 4A3BE 4BY7E 3M3YE 3S1NE 2NVQE 3GTQE 1TWFE 4A3ME 3GTJE 5IYCE 5M3ME 2R92E 3PO3E 3M4OE 2PMZH 5M5XE 1Y1WE 3GTGE 3S15E 4A3LE 3GTOE 1Y1VE 5M5WE 1EIKA 1K83E 3RZDE 3I4ME 2E2IE 2WB1H 4QIWH 3S2HE 3CQZE 2JA6E 5C3EE 5IYDE 3HOYE 4A3DE 5C44E 3HOVE 3K7AE 4A3KE 4A93E 5M5YE 4A3JE 1I50E 2R7ZE 3S14E 5IP9E 3S16E 3GTKE 2NVYE 3FKIE 3H0GE 4Y52E 1TWGE 1I3QE 4BY1E
chains in the Genus database with same CATH superfamily
5C4XE 3S1RE 1K83F 3RZDF 1WCME 3S2DE 2JA7E 2E2IF 3GTPF 5BYHE 2R93E 3I4MF 3S2HF 2JA6F 4AYBH 3HOZF 5C3EF 5IYDF 3HOYF 4A3DF 5C44F 1TWAE 4A3CE 4A3FE 3WODE 1YNNK 2YU9F 3HOVF 2JA5F 4OIQE 3K7AF 2VUME 3H3VF 5IPLE 1SFOE 4ZH4E 4A3KF 4A3BF 4YFKE 4MEXE 2Y0SI 5IP7E 2E2JE 4XLNE 4Y7NE 4A93F 5M5YF 4A3JF 3I4NE 4C3HE 1I50F 2B63E 5IYCF 3HOWE 2WAQK 4C2ME 5FJ8E 3S17E 4JK1E 4KN4E 5IP9F 5C4JE 4C3JE 3PO3F 3GTKF 4GZYE 4BBRE 4A3GE 2NVYF 3FKIF 4YFNE 3S15F 5M3FE 3PO2E 4BXXE 4X6AE 3H0GF 5IYBE 3GTOF 2WAQH 1TWGF 1TWHE 5M5WF 1I3QF 4BY1F 4OIOE 2JA8E 3GTME 2A6HE 3S1QE 3CQZF 4LK1E 5C4XF 3S1RF 4G7ZE 4BBSE 3S1ME 1WCMF 3S2DF 2JA7F 3HOXE 2R93F 4XLPE 4A3IE 5FLME 1TWAF 4A3CF 2E2HE 1SMYE 4OIPE 4A3EE 4YG2E 4A3FF 5D4DE 2BE5E 2WB1I 2O5JE 4LJZE 1SFOF 1DZFA 5IP7F 2E2JF 4XSXE 3GTLE 2A68E 3HKZK 4Q4ZE 3S14F 2Y0SH 3GTPE 3I4NF 3S16F 1TWCE 3HOUE 2B63F 4C2MF 5FJ8F 2A69E 3HOZE 5C4JF 4C3JF 2NVXE 4Y52F 3HKZH 2YU9E 4BBRF 4MQ9E 5TMFE 5M3FF 3PO2F 4BXXF 2JA5E 3H3VG 5IYBF 4X6AF 1R9TE 2NVTE 1I6HE 4C3IE 3RZOE 1QKLA 4A3BE 4G7OE 4BY7E 2JA8F 3GTMF 3M3YE 1ZYRE 2PMZK 3S1NE 3S1QF 2NVQE 3GTQE 1YNJK 1TWFE 2O5IE 3S1MF 4A3ME 3GTJE 2KRXA 4XSZE 5IYCE 5M3ME 2R92E 3PO3E 3M4OE 2PMZH 5FLMF 4QIWK 5M5XE 1Y1WE 3GTGE 2VUMF 3S15E 4MEYE 4A3LE 3GTOE 1Y1VE 5M5WE 4Y7NF 1EIKA 1K83E 3RZDE 3I4ME 2E2IE 2WB1H 4KN7E 4QIWH 4C3HF 3S2HE 3CQZE 4Q5SE 3GTLF 5D4CE 3HOWF 3EQLE 3S17F 2JA6E 4LLGE 5C3EE 5IYDE 3HOYE 4A3DE 5C44E 1TWCF 4LK0E 2PPBE 3HOUF 4A3GF 3HOVE 2NVXF 4G7HE 3K7AE 5D4EE 4YFXE 1TWHF 4A3KE 2A6EE 1R9TF 1I6HF 2NVTF 4C3IF 3RZOF 4A93E 2CW0E 4OIRE 4BBSF 5M5YE 4A3JE 4BY7F 1I50E 3HOXF 3M3YF 2R7ZE 3S1NF 5E18E 2NVQF 1IW7E 3S14E 5IP9E 1TWFF 3GTQF 4A3MF 3S16E 3GTJF 4OINE 3GTKE 4A3IF 2NVYE 1HQME 3FKIE 5M3MF 3DXJE 2E2HF 3H0GE 4A3EF 4KMUE 2R92F 3M4OF 4Y52E 5M5XF 1Y1WF 3GTGF 1TWGE 5E17E 5TMCE 1I3QE 4BY1E 2R7ZF 4A3LF 4AYBK 1I6VE 1Y1VF
chains in the Genus database with same CATH topology
5C4XE 3S1RE 1WCME 3S2DE 2JA7E 2R93E 4AYBH 1TWAE 4A3CE 4A3FE 2VUME 3H3VF 1SFOE 5IP7E 2E2JE 4Y7NE 3I4NE 4C3HE 2B63E 3HOWE 4C2ME 5FJ8E 3S17E 5C4JE 4C3JE 4BBRE 4A3GE 5M3FE 3PO2E 4BXXE 4X6AE 5IYBE 2WAQH 1TWHE 2JA8E 3GTME 3S1QE 4BBSE 3S1ME 3HOXE 4A3IE 5FLME 2E2HE 4A3EE 1DZFA 3GTLE 2Y0SH 3GTPE 1TWCE 3HOUE 3HOZE 2NVXE 3HKZH 2YU9E 2JA5E 1R9TE 2NVTE 1I6HE 4C3IE 3RZOE 4A3BE 4BY7E 3M3YE 3S1NE 2NVQE 3GTQE 1TWFE 4A3ME 3GTJE 5IYCE 5M3ME 2R92E 3PO3E 3M4OE 2PMZH 5M5XE 1Y1WE 3GTGE 3S15E 4A3LE 3GTOE 1Y1VE 5M5WE 1EIKA 1K83E 3RZDE 3I4ME 2E2IE 2WB1H 4QIWH 3S2HE 3CQZE 2JA6E 5C3EE 5IYDE 3HOYE 4A3DE 5C44E 3HOVE 3K7AE 4A3KE 4A93E 5M5YE 4A3JE 1I50E 2R7ZE 3S14E 5IP9E 3S16E 3GTKE 2NVYE 3FKIE 3H0GE 4Y52E 1TWGE 1I3QE 4BY1E
chains in the Genus database with same CATH homology


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