4A3BE

Rna polymerase ii initial transcribing complex with a 4nt dna-rna hybrid
Total Genus 62
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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
62
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 Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule tags Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
total genus 62
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-09-30

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 4a3bE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4a3bE02
4C3HE 4C3JE 2YU9E 3GTOE 1Y1WE 5M3FE 1R9TE 2JA6E 3S14E 3S2DE 3GTJE 4A3KE 5FLME 4A3FE 3S1ME 4A3CE 5C4XE 1I6HE 5IYCE 4A3ME 1TWAE 5C3EE 3RZDE 3HOWE 3I4NE 2WB1H 4Y52E 1TWFE 3HOUE 3H0GE 1I3QE 2VUME 3FKIE 3GTKE 2JA8E 1TWCE 3HOVE 3HKZH 2R93E 3GTGE 2E2HE 4BY1E 3PO3E 2E2IE 3S1NE 4X6AE 4BY7E 2NVYE 5IP9E 2Y0SH 2JA7E 4A3BE 5M3ME 2JA5E 2R92E 5IYDE 1DZFA 3S16E 2B63E 1WCME 3GTME 3GTQE 5M5XE 4BBRE 3H3VF 5C44E 3GTPE 3M4OE 1K83E 3HOZE 3M3YE 2R7ZE 4BBSE 4A3JE 3I4ME 3CQZE 3S17E 4A93E 2WAQH 4C3IE 2PMZH 4A3DE 1TWHE 1EIKA 4AYBH 5IYBE 3PO2E 4QIWH 2NVQE 1TWGE 3S15E 5IP7E 1I50E 3RZOE 1SFOE 3K7AE 5M5WE 4BXXE 4A3LE 4A3GE 5M5YE 3S1QE 5FJ8E 2E2JE 1Y1VE 3HOYE 3S2HE 3S1RE 2NVXE 4A3EE 4Y7NE 3HOXE 4C2ME 4A3IE 2NVTE 3GTLE 5C4JE
chains in the Genus database with same CATH superfamily
4C3HE 4C3JE 2YU9E 1I6VE 3S1NF 3GTOE 1Y1WE 5M3FE 1R9TE 2JA6E 3H3VG 5C4JF 3M3YF 3S14E 4QIWK 1I3QF 3S2DE 3GTJE 4A3KE 4Y7NF 3HOXF 5M5XF 2NVXF 3GTLF 3HOZF 5FLME 4A3FE 3S1ME 4A3CE 5C4XE 1SMYE 5C44F 1I6HE 3DXJE 3HOWF 1WCMF 3M4OF 2B63F 5IYCE 4A3ME 3S1QF 4OIOE 1TWAE 5C3EE 3RZDE 3HOWE 3S1MF 4A3CF 1Y1VF 3HOYF 3I4NE 5D4EE 4A3MF 3K7AF 1HQME 1SFOF 2KRXA 2JA5F 4OIRE 2WB1H 2Y0SI 4Y52E 2O5JE 4A3LF 4X6AF 4Q5SE 1TWFE 3GTJF 5M3FF 3HOUE 3WODE 4A3KF 5IP9F 1R9TF 4GZYE 4BY7F 3H0GE 1I3QE 2VUME 1YNNK 2JA6F 4C3IF 3FKIE 4Q4ZE 3H0GF 4C2MF 4C3JF 3GTKE 4BBSF 1ZYRE 4YFXE 4A93F 4Y52F 2JA8E 4G7HE 2CW0E 2E2JF 3S2HF 1TWCE 4JK1E 4LK0E 4A3JF 3I4MF 2BE5E 3HKZK 1TWFF 2WAQK 5BYHE 3S1RF 3GTQF 5M5YF 1K83F 4YG2E 5C3EF 3RZDF 3EQLE 4LJZE 3HOVE 4LLGE 4YFNE 3HKZH 2R93E 3RZOF 5M3MF 2A6HE 3GTGE 1I50F 2R92F 4YFKE 5FLMF 1TWGF 4A3FF 4BXXF 5IYCF 5TMCE 2PPBE 2E2HE 2NVYF 4XSXE 4G7OE 4BY1E 4KN7E 2NVQF 3S15F 3PO3E 4LK1E 5E17E 5E18E 2E2IE 3S17F 3S1NE 4AYBK 2YU9F 4C3HF 3S14F 4A3DF 3PO3F 4MEYE 4X6AE 1QKLA 1Y1WF 2NVTF 3GTPF 4BY7E 2NVYE 5IP9E 2WB1I 2Y0SH 4MEXE 2E2HF 2JA7E 5D4DE 3I4NF 4XLPE 4A3BE 2O5IE 2A68E 1IW7E 4BY1F 5M3ME 2JA5E 2R92E 5IYDE 1DZFA 4KMUE 3S16E 2B63E 3HOVF 1WCME 3GTME 5TMFE 4ZH4E 3GTQE 1TWAF 2A69E 5M5XE 4BBRE 5FJ8F 4G7ZE 5IPLE 3H3VF 5C44E 3GTPE 3M4OE 1K83E 5IP7F 5D4CE 3HOZE 3M3YE 2R7ZE 2PMZK 4KN4E 4BBSE 2JA7F 4A3JE 3I4ME 1TWCF 3CQZE 3S17E 1TWHF 4A93E 2E2IF 1YNJK 2WAQH 4C3IE 2PMZH 3PO2F 4A3DE 4OIQE 3GTKF 1TWHE 3GTOF 1EIKA 4AYBH 3FKIF 3HOUF 5IYBE 4OIPE 3PO2E 4A3EF 4QIWH 2R7ZF 2NVQE 1TWGE 3S15E 2VUMF 5IP7E 4A3IF 1I50E 3GTGF 3CQZF 3RZOE 4OINE 1SFOE 3K7AE 5M5WE 4BXXE 4A3LE 4A3GE 5M5YE 2R93F 3S1QE 5M5WF 5FJ8E 4BBRF 5IYDF 2E2JE 1Y1VE 3HOYE 3S2HE 2JA8F 4A3GF 2A6EE 4A3BF 3GTMF 3S1RE 2NVXE 4A3EE 4Y7NE 3HOXE 5IYBF 4XSZE 3S16F 4C2ME 3S2DF 4XLNE 1I6HF 4A3IE 5C4XF 2NVTE 4MQ9E 3GTLE 5C4JE
chains in the Genus database with same CATH topology
4C3HE 4C3JE 2YU9E 3GTOE 1Y1WE 5M3FE 1R9TE 2JA6E 3S14E 3S2DE 3GTJE 4A3KE 5FLME 4A3FE 3S1ME 4A3CE 5C4XE 1I6HE 5IYCE 4A3ME 1TWAE 5C3EE 3RZDE 3HOWE 3I4NE 2WB1H 4Y52E 1TWFE 3HOUE 3H0GE 1I3QE 2VUME 3FKIE 3GTKE 2JA8E 1TWCE 3HOVE 3HKZH 2R93E 3GTGE 2E2HE 4BY1E 3PO3E 2E2IE 3S1NE 4X6AE 4BY7E 2NVYE 5IP9E 2Y0SH 2JA7E 4A3BE 5M3ME 2JA5E 2R92E 5IYDE 1DZFA 3S16E 2B63E 1WCME 3GTME 3GTQE 5M5XE 4BBRE 3H3VF 5C44E 3GTPE 3M4OE 1K83E 3HOZE 3M3YE 2R7ZE 4BBSE 4A3JE 3I4ME 3CQZE 3S17E 4A93E 2WAQH 4C3IE 2PMZH 4A3DE 1TWHE 1EIKA 4AYBH 5IYBE 3PO2E 4QIWH 2NVQE 1TWGE 3S15E 5IP7E 1I50E 3RZOE 1SFOE 3K7AE 5M5WE 4BXXE 4A3LE 4A3GE 5M5YE 3S1QE 5FJ8E 2E2JE 1Y1VE 3HOYE 3S2HE 3S1RE 2NVXE 4A3EE 4Y7NE 3HOXE 4C2ME 4A3IE 2NVTE 3GTLE 5C4JE
chains in the Genus database with same CATH homology


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