3S1NF

Rna polymerase ii initiation complex with a 5-nt rna (variant 2)
Total Genus 23
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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
23
sequence length
85
structure length
85
Chain Sequence
EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Loading diagram...

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 23
structure length 85
sequence length 85
ec nomenclature
pdb deposition date 2011-05-15

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
F PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit Eukaryotic RPB6 RNA polymerase subunit 3s1nF00
2R92F 5D4EE 1YNNK 1I6HF 4G7ZE 4A3EF 4YFXE 3PO3F 1I50F 4A3FF 1Y1VF 4LK0E 2A68E 4LK1E 5IYBF 4MEXE 3HOUF 3S2HF 4OIQE 1HQME 2JA6F 2BE5E 2E2HF 4A3JF 4AYBK 4BXXF 5IP9F 4A3CF 4OIPE 3WODE 5D4DE 4OINE 5M5WF 1I3QF 1ZYRE 3FKIF 2PMZK 4XLNE 4A93F 1R9TF 3GTMF 2YU9F 4BBRF 5TMCE 3RZOF 2JA7F 3S17F 4A3BF 5M5XF 4Q5SE 4LJZE 3HOWF 4XLPE 3I4MF 5C4XF 4A3MF 1YNJK 2O5IE 2A6EE 2NVQF 4GZYE 3GTJF 4OIRE 3M3YF 3HOZF 2R93F 4LLGE 4BY7F 4YG2E 4A3GF 5C3EF 1TWHF 3K7AF 3GTPF 5IYCF 1TWFF 4KN4E 4G7OE 2NVYF 4ZH4E 3I4NF 2Y0SI 3S16F 5C4JF 1I6VE 2CW0E 3H0GF 4Y52F 4C3HF 2WB1I 2A69E 3GTOF 2PPBE 3S2DF 3S15F 3S1QF 5M3MF 2NVXF 4A3DF 1TWCF 4XSXE 4OIOE 3GTQF 2E2JF 3S1RF 2JA5F 2VUMF 4A3IF 2B63F 1TWGF 4C3IF 3S1MF 4C3JF 4YFNE 5IP7F 4Y7NF 2R7ZF 5IYDF 3HKZK 3PO2F 5C44F 5D4CE 5IPLE 3HOVF 3CQZF 3M4OF 3HOYF 1SMYE 5BYHE 4A3LF 2A6HE 3GTLF 3S14F 3EQLE 4Q4ZE 1WCMF 1SFOF 4KMUE 1TWAF 4XSZE 4G7HE 1Y1WF 3H3VG 4C2MF 2WAQK 3GTKF 4KN7E 4MQ9E 4JK1E 4YFKE 2O5JE 5E18E 3DXJE 5TMFE 2JA8F 5FLMF 4BY1F 3HOXF 5M3FF 4BBSF 1QKLA 4A3KF 5FJ8F 1K83F 3GTGF 3RZDF 2NVTF 4MEYE 4X6AF 2E2IF 3S1NF 5E17E 1IW7E 5M5YF
chains in the Genus database with same CATH superfamily
5C44E 5D4EE 1YNNK 1I6HF 2R92F 4G7ZE 4A3EF 4YFXE 5IYDE 1I50F 4A3FF 3PO3F 1Y1VF 4LK0E 2A68E 2WB1H 4LK1E 5IYBF 4MEXE 3HOUF 3S2HF 4C3JE 5IP7E 1HQME 4OIQE 2JA6F 2BE5E 2E2HF 4A3JF 4AYBK 4C3IE 3HOVE 3S1ME 4BXXF 5IP9F 4A3CF 4OIPE 4A3IE 3WODE 5D4DE 4OINE 5M5WF 3PO2E 2R7ZE 1I3QF 1TWCE 1ZYRE 2PMZK 3FKIF 4XLNE 4Y7NE 4A93F 4A3DE 3HKZH 1R9TF 2NVXE 3GTMF 2YU9F 3S1QE 4BBRF 5TMCE 3RZOF 1TWGE 2Y0SH 2B63E 2JA7F 3S17F 4C3HE 4A3BF 2VUME 2KRXA 5M5XF 3S1RE 2JA5E 4Y52E 4Q5SE 2E2JE 4LJZE 3GTQE 3HOWF 4XLPE 3I4MF 5C4XF 4A3MF 3I4NE 1YNJK 2O5IE 2A6EE 2NVQF 4GZYE 5M3ME 3GTJF 4OIRE 3HOZF 3M3YF 3S15E 3GTOE 3S2DE 2R93F 4LLGE 3K7AE 4BY7F 3H0GE 4YG2E 1TWHE 4A3GF 5C3EE 5C4JE 3S16E 5C3EF 1TWHF 2NVYE 3K7AF 4BY7E 1TWFE 5IYCE 3GTPF 5IYCF 3GTPE 1TWFF 4AYBH 2NVQE 4KN4E 4G7OE 2NVYF 4ZH4E 4A3ME 2Y0SI 3I4NF 5C4XE 1DZFA 3S16F 3I4ME 5C4JF 1I6VE 2CW0E 4A3GE 3H0GF 5M5XE 4Y52F 4C3HF 4A3BE 2WB1I 2A69E 3S17E 3GTOF 3RZOE 2PPBE 3S2DF 3S15F 3HOZE 5M3MF 3GTJE 2YU9E 3M3YE 3S1QF 2NVXF 3GTME 4A3DF 1TWCF 1I3QE 4XSXE 4OIOE 3HOWE 3GTQF 2E2JF 3S1RF 2JA5F 2VUMF 4A3IF 2B63F 1TWGF 2JA7E 4BBRE 4C3IF 4A3JE 2JA6E 3S1MF 1R9TE 4C3JF 4YFNE 5IP7F 4A93E 4Y7NF 1Y1VE 5IYBE 3FKIE 3S2HE 4A3FE 2R7ZF 5IYDF 3HKZK 5M5WE 3PO3E 3PO2F 1I6HE 5C44F 2R92E 5D4CE 5IPLE 5IP9E 4BXXE 4A3CE 2PMZH 2E2HE 3HOVF 3HOUE 3CQZF 3M4OF 3HOYF 2R93E 1SMYE 5BYHE 4X6AE 1I50E 4A3EE 4A3LF 2A6HE 3RZDE 1K83E 5FJ8E 2NVTE 3EQLE 3GTLF 3S14F 5M5YE 4Q4ZE 1WCMF 5M3FE 3HOXE 4KMUE 1SFOF 5FLME 1TWAF 3S1NE 4XSZE 2E2IE 4G7HE 1Y1WF 3H3VG 4C2MF 2WAQK 3GTKF 3GTGE 4KN7E 4A3KE 3GTKE 4BBSE 4MQ9E 4BY1E 4JK1E 4QIWK 4YFKE 2JA8E 2O5JE 3DXJE 5TMFE 5E18E 2JA8F 5FLMF 4BY1F 3HOXF 1SFOE 5M3FF 1WCME 2WAQH 4BBSF 1QKLA 4A3KF 5FJ8F 1K83F 3GTLE 3RZDF 2NVTF 3GTGF 3S14E 4A3LE 1EIKA 4MEYE 4C2ME 4X6AF 1Y1WE 3M4OE 3CQZE 2E2IF 3HOYE 3S1NF 1TWAE 5E17E 1IW7E 3H3VF 5M5YF 4QIWH
chains in the Genus database with same CATH topology
2R92F 5D4EE 1YNNK 1I6HF 4G7ZE 4A3EF 4YFXE 3PO3F 1I50F 4A3FF 1Y1VF 4LK0E 2A68E 4LK1E 5IYBF 4MEXE 3HOUF 3S2HF 4OIQE 1HQME 2JA6F 2BE5E 2E2HF 4A3JF 4AYBK 4BXXF 5IP9F 4A3CF 4OIPE 3WODE 5D4DE 4OINE 5M5WF 1I3QF 1ZYRE 3FKIF 2PMZK 4XLNE 4A93F 1R9TF 3GTMF 2YU9F 4BBRF 5TMCE 3RZOF 2JA7F 3S17F 4A3BF 2KRXA 5M5XF 4Q5SE 4LJZE 3HOWF 4XLPE 3I4MF 5C4XF 4A3MF 1YNJK 2O5IE 2A6EE 2NVQF 4GZYE 3GTJF 4OIRE 3M3YF 3HOZF 2R93F 4LLGE 4BY7F 4YG2E 4A3GF 5C3EF 1TWHF 3K7AF 3GTPF 5IYCF 1TWFF 4KN4E 4G7OE 2NVYF 4ZH4E 3I4NF 2Y0SI 3S16F 5C4JF 1I6VE 2CW0E 3H0GF 4Y52F 4C3HF 2WB1I 2A69E 3GTOF 2PPBE 3S2DF 3S15F 3S1QF 5M3MF 2NVXF 4A3DF 1TWCF 4XSXE 4OIOE 3GTQF 2E2JF 3S1RF 2JA5F 2VUMF 4A3IF 2B63F 1TWGF 4C3IF 3S1MF 4C3JF 4YFNE 5IP7F 4Y7NF 2R7ZF 5IYDF 3HKZK 3PO2F 5C44F 5D4CE 5IPLE 3HOVF 3CQZF 3M4OF 3HOYF 1SMYE 5BYHE 4A3LF 2A6HE 3GTLF 3S14F 3EQLE 4Q4ZE 1WCMF 1SFOF 4KMUE 1TWAF 4XSZE 4G7HE 1Y1WF 3H3VG 4C2MF 2WAQK 3GTKF 4KN7E 4MQ9E 4JK1E 4QIWK 4YFKE 2O5JE 5E18E 3DXJE 5TMFE 2JA8F 5FLMF 4BY1F 3HOXF 5M3FF 4BBSF 1QKLA 4A3KF 5FJ8F 1K83F 3GTGF 3RZDF 2NVTF 4MEYE 4X6AF 2E2IF 3S1NF 5E17E 1IW7E 5M5YF
chains in the Genus database with same CATH homology


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