4A3CE

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid
Total Genus 69
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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
69
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 69
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 4a3cE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4a3cE02
4X6AE 4C3HE 5M3ME 3RZOE 1TWHE 3S15E 5M3FE 1I6HE 5C4XE 3GTJE 2E2HE 2JA8E 1WCME 3GTGE 3HOVE 4A93E 2E2JE 3GTLE 5IYCE 2NVQE 5IP9E 1K83E 4A3IE 3S16E 2NVXE 4A3CE 1EIKA 1TWCE 2R93E 1Y1WE 4QIWH 4BBSE 1DZFA 4C3JE 4Y52E 3HKZH 3S2DE 4A3JE 4BY7E 4A3BE 3M4OE 4C3IE 4BY1E 3FKIE 3HOUE 2NVTE 2E2IE 5M5XE 3H3VF 3GTME 4A3KE 3S17E 2JA7E 3GTQE 2WB1H 3M3YE 2Y0SH 4A3ME 1TWAE 3GTOE 1SFOE 2R92E 2PMZH 4BBRE 5IP7E 2YU9E 4A3GE 4AYBH 5C3EE 4C2ME 3PO2E 2NVYE 5C44E 3HOXE 3HOZE 3RZDE 3S14E 5M5YE 4Y7NE 4A3EE 3I4ME 1TWGE 2JA6E 5C4JE 1R9TE 2B63E 4A3DE 1I50E 3CQZE 1I3QE 5IYBE 3S1NE 3S1ME 5FJ8E 3GTKE 5M5WE 3GTPE 4A3LE 3HOYE 3S1RE 2R7ZE 2VUME 5FLME 3K7AE 2WAQH 3H0GE 3HOWE 2JA5E 5IYDE 1Y1VE 1TWFE 4A3FE 3S1QE 3I4NE 3PO3E 3S2HE 4BXXE
chains in the Genus database with same CATH superfamily
4X6AE 4C3HE 5C4JF 5M3ME 3RZOE 4XLNE 1Y1WF 2R93F 1TWHE 3S15E 5M3FE 1I6HE 5C4XE 3GTJE 2JA6F 3PO2F 4C2MF 2E2HE 2JA8E 4LK0E 4XLPE 4LLGE 1WCME 3GTGE 4A3GF 2PMZK 4G7ZE 3HOVE 4A93E 2E2JE 3GTLE 1SFOF 5E17E 4Q5SE 1TWHF 5IYCE 2NVQE 3DXJE 5M3MF 3M3YF 4C3HF 3GTQF 4BXXF 1QKLA 5IP9E 5IYCF 5E18E 2JA7F 3GTLF 3S17F 2A6HE 3HOVF 1K83E 4A3IE 2A69E 3WODE 1WCMF 4YFKE 3S16E 2NVXE 4A3CE 1Y1VF 5TMFE 2E2IF 5IP7F 1TWCE 5IYDF 1EIKA 4MEYE 3GTJF 3HOWF 1TWAF 2NVTF 2WB1I 2R93E 1YNJK 1Y1WE 4Q4ZE 2BE5E 3FKIF 4QIWH 5FLMF 3RZOF 4BBSE 4X6AF 1DZFA 1IW7E 3HKZK 4G7OE 3PO3F 4C3JE 3I4NF 4Y52E 3HKZH 4YFNE 3S2DE 1TWFF 5D4DE 4KN4E 4A3JE 4A3FF 3S1RF 4BY7E 4ZH4E 4A3BF 2O5IE 4A3BE 3HOUF 3K7AF 3M4OE 5M5WF 4BY1F 4C3IE 2WAQK 4BY1E 4BBSF 4G7HE 3FKIE 3M4OF 2CW0E 3HOUE 2NVTE 1HQME 1TWGF 2PPBE 2E2IE 5M5XE 2NVXF 4BY7F 3GTPF 3H3VF 2Y0SI 3GTME 4KMUE 4OIPE 4Y52F 4A3KE 5FJ8F 4C3JF 3S17E 3S1MF 3HOZF 2JA7E 1I3QF 5IP9F 2KRXA 3GTQE 3EQLE 2WB1H 4MEXE 3M3YE 4GZYE 2Y0SH 4QIWK 2NVQF 4A3ME 1TWAE 5BYHE 3GTOE 1SFOE 2R92E 2PMZH 4BBRE 5D4CE 5IP7E 2E2JF 3I4MF 2YU9E 4A3GE 3S16F 4AYBH 5C3EE 4A3CF 2YU9F 4A3IF 1SMYE 4C2ME 3PO2E 5M3FF 1I6HF 5C4XF 5IPLE 2NVYF 5C44F 2NVYE 5C44E 4OIOE 3HOXE 5TMCE 1I6VE 4JK1E 4XSZE 3HOZE 3S2HF 3RZDE 4A93F 3S14E 3S1QF 3GTMF 2A68E 3GTGF 5C3EF 1ZYRE 4XSXE 5M5YE 4Y7NE 4A3EE 3I4ME 4BBRF 2E2HF 2JA5F 2JA8F 1TWGE 2R92F 3GTOF 2JA6E 4OIQE 4A3MF 3H3VG 3S15F 4YFXE 5C4JE 4A3DF 1R9TE 2B63E 4A3DE 1I50E 3CQZE 1I3QE 5IYBE 3S1NE 4C3IF 3S1ME 5FJ8E 4A3KF 3GTKE 4MQ9E 5M5WE 3GTPE 4YG2E 5M5XF 4A3LF 3H0GF 4A3LE 3HOYE 4OIRE 3S1RE 2R7ZE 5D4EE 4A3JF 3S2DF 2A6EE 2VUME 4LK1E 2VUMF 1I50F 3CQZF 1R9TF 2B63F 5FLME 2R7ZF 3K7AE 1YNNK 2WAQH 3HOYF 3H0GE 3HOWE 2JA5E 4OINE 4KN7E 2O5JE 5IYDE 1TWCF 4Y7NF 5M5YF 1Y1VE 4A3EF 1TWFE 4A3FE 3S1QE 4AYBK 1K83F 3I4NE 3GTKF 3S14F 3RZDF 3PO3E 3S2HE 5IYBF 3S1NF 3HOXF 4BXXE 4LJZE
chains in the Genus database with same CATH topology
4X6AE 4C3HE 5M3ME 3RZOE 1TWHE 3S15E 5M3FE 1I6HE 5C4XE 3GTJE 2E2HE 2JA8E 1WCME 3GTGE 3HOVE 4A93E 2E2JE 3GTLE 5IYCE 2NVQE 5IP9E 1K83E 4A3IE 3S16E 2NVXE 4A3CE 1EIKA 1TWCE 2R93E 1Y1WE 4QIWH 4BBSE 1DZFA 4C3JE 4Y52E 3HKZH 3S2DE 4A3JE 4BY7E 4A3BE 3M4OE 4C3IE 4BY1E 3FKIE 3HOUE 2NVTE 2E2IE 5M5XE 3H3VF 3GTME 4A3KE 3S17E 2JA7E 3GTQE 2WB1H 3M3YE 2Y0SH 4A3ME 1TWAE 3GTOE 1SFOE 2R92E 2PMZH 4BBRE 5IP7E 2YU9E 4A3GE 4AYBH 5C3EE 4C2ME 3PO2E 2NVYE 5C44E 3HOXE 3HOZE 3RZDE 3S14E 5M5YE 4Y7NE 4A3EE 3I4ME 1TWGE 2JA6E 5C4JE 1R9TE 2B63E 4A3DE 1I50E 3CQZE 1I3QE 5IYBE 3S1NE 3S1ME 5FJ8E 3GTKE 5M5WE 3GTPE 4A3LE 3HOYE 3S1RE 2R7ZE 2VUME 5FLME 3K7AE 2WAQH 3H0GE 3HOWE 2JA5E 5IYDE 1Y1VE 1TWFE 4A3FE 3S1QE 3I4NE 3PO3E 3S2HE 4BXXE
chains in the Genus database with same CATH homology


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