3S1MF

Rna polymerase ii initiation complex with a 5-nt rna (variant 1)
Total Genus 19
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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
19
sequence length
85
structure length
85
Chain Sequence
EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
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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 19
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 3s1mF00
4KN7E 4ZH4E 4LJZE 3I4MF 1I6VE 3GTPF 4BXXF 2R7ZF 4BBRF 4LK1E 1YNNK 4MEYE 2JA6F 3HOXF 2WAQK 3GTGF 1I6HF 4KMUE 5C4JF 5FLMF 3HOUF 3S1QF 3GTOF 2R93F 2NVYF 5IP9F 3HOZF 3S1RF 3M3YF 1TWFF 5IPLE 2E2HF 4YFNE 1ZYRE 4XSZE 5IYCF 4Q4ZE 4OIQE 4A3BF 4OIPE 3HOVF 4XLNE 3EQLE 1TWHF 1SMYE 5M3FF 3WODE 3S16F 2BE5E 3S1MF 3K7AF 4A3LF 2NVTF 5C4XF 4BY7F 3S2HF 2O5IE 4KN4E 4C3JF 5C3EF 3GTKF 5TMCE 4OIOE 3CQZF 5IYBF 4Y7NF 2VUMF 2O5JE 2JA8F 3PO3F 1WCMF 2A6EE 5BYHE 1SFOF 2CW0E 3S1NF 2A68E 4JK1E 4AYBK 2JA7F 4A3GF 4A3IF 5E17E 1TWCF 2NVQF 5D4DE 3GTMF 4A3KF 2A6HE 4OINE 1I3QF 4LLGE 3I4NF 3RZDF 5E18E 5M5YF 4BY1F 4A3MF 4MQ9E 2E2IF 4LK0E 3RZOF 3PO2F 4G7HE 4Q5SE 5IYDF 1R9TF 3GTQF 4OIRE 1K83F 2E2JF 4A3CF 4C3IF 4YFKE 4YG2E 5TMFE 4A3DF 1IW7E 5M5XF 3M4OF 4X6AF 5D4EE 2NVXF 2WB1I 3HOWF 4A93F 4C2MF 3GTLF 3HKZK 4G7OE 1TWGF 4Y52F 4YFXE 1QKLA 4XSXE 5M5WF 5D4CE 4A3FF 4A3EF 3S17F 2R92F 3S15F 1HQME 2PPBE 5M3MF 1Y1WF 4GZYE 2YU9F 3HOYF 2Y0SI 4XLPE 1I50F 4MEXE 2A69E 1TWAF 3GTJF 4C3HF 3H3VG 1Y1VF 3DXJE 3H0GF 4A3JF 3S14F 4G7ZE 5FJ8F 1YNJK 4BBSF 5C44F 5IP7F 2PMZK 3S2DF 2JA5F 3FKIF 2B63F
chains in the Genus database with same CATH superfamily
1Y1VE 4KN7E 2WB1H 4ZH4E 4LJZE 3I4MF 1I6VE 3H0GE 3GTPF 4BXXF 4A3JE 4QIWH 3S14E 2R7ZF 4BBRF 4LK1E 5FJ8E 1YNNK 4MEYE 4BBSE 5C44E 3HOXF 2WAQK 5IP7E 2JA6F 3GTGF 1I6HF 2JA5F 3S2DE 2JA5E 3FKIE 3HOVE 4KMUE 2B63E 5C4JF 3I4ME 3GTPE 4BXXE 5FLMF 2R7ZE 4BBRE 3GTOF 3HOUF 3S1QF 2R93F 2NVYF 5IP9F 2Y0SH 3HOZF 2WAQH 3S1RF 2JA6E 3HOXE 3GTGE 3M3YF 1I6HE 1TWFF 5IPLE 2E2HF 4YFNE 1ZYRE 5C4JE 4XSZE 3H3VF 5IYCF 4Q4ZE 4OIQE 4A3BF 4OIPE 5FLME 3HOVF 4XLNE 3EQLE 3HOUE 3GTOE 1TWHF 3S1QE 2NVYE 2R93E 1SMYE 5IP9E 3HOZE 4AYBH 5M3FF 3S1RE 3M3YE 3WODE 3S16F 1TWFE 2BE5E 3S1MF 3K7AF 4A3LF 2NVTF 2E2HE 5C4XF 5IYCE 4BY7F 3S2HF 2O5IE 4A3BE 4KN4E 4C3JF 1TWHE 5C3EF 3GTKF 5M3FE 5TMCE 4OIOE 3CQZF 5IYBF 4Y7NF 2VUMF 3S16E 2O5JE 2JA8F 3PO3F 3K7AE 1WCMF 4A3LE 2A6EE 5BYHE 1SFOF 2NVTE 2CW0E 3S1NF 2A68E 5C4XE 4JK1E 4AYBK 2JA7F 1DZFA 4A3GF 3S2HE 4BY7E 4C3JE 4A3IF 5E17E 5C3EE 3GTKE 1TWCF 2NVQF 3CQZE 5IYBE 4Y7NE 5D4DE 2VUME 3GTMF 2JA8E 3PO3E 1WCME 4A3KF 1SFOE 2A6HE 3S1NE 4OINE 1I3QF 4LLGE 3I4NF 3RZDF 2JA7E 3HKZH 5E18E 4A3GE 5M5YF 4BY1F 4A3IE 4A3MF 4MQ9E 2E2IF 4LK0E 3RZOF 3PO2F 1TWCE 4G7HE 2NVQE 4Q5SE 5IYDF 1R9TF 3GTME 3GTQF 4OIRE 1K83F 4A3KE 2E2JF 4A3CF 2B63F 1I3QE 3I4NE 4C3IF 3RZDE 4YFKE 4YG2E 5TMFE 5M5YE 4A3DF 1IW7E 5M5XF 3M4OF 3S1ME 4X6AF 5D4EE 4BY1E 4A3ME 2E2IE 2NVXF 2WB1I 3HOWF 4A93F 3RZOE 3PO2E 4C2MF 3GTLF 3HKZK 1R9TE 5IYDE 4G7OE 3GTQE 1TWGF 1K83E 2E2JE 4Y52F 4YFXE 4A3CE 1QKLA 4XSXE 4C3IE 4A3DE 5M5WF 5M5XE 5D4CE 3M4OE 4A3FF 4X6AE 4A3EF 3S17F 2PMZH 2NVXE 2R92F 3HOWE 1HQME 3S15F 4A93E 2PPBE 5M3MF 4C2ME 1Y1WF 3GTLE 4GZYE 2YU9F 3HOYF 1TWGE 2Y0SI 4XLPE 1I50F 4Y52E 4MEXE 2A69E 1TWAF 5M5WE 4C3HF 3GTJF 3H3VG 1EIKA 1Y1VF 4A3FE 3DXJE 4A3EE 3S17E 1TWAE 3H0GF 3S15E 2R92E 4A3JF 3S14F 2KRXA 5M3ME 1Y1WE 4QIWK 4G7ZE 5FJ8F 1YNJK 2YU9E 3HOYE 4BBSF 5C44F 1I50E 5IP7F 2PMZK 3S2DF 3GTJE 3FKIF 4C3HE
chains in the Genus database with same CATH topology
4KN7E 4ZH4E 4LJZE 3I4MF 1I6VE 3GTPF 4BXXF 2R7ZF 4BBRF 4LK1E 1YNNK 4MEYE 2JA6F 3HOXF 2WAQK 3GTGF 1I6HF 4KMUE 5C4JF 5FLMF 3HOUF 3S1QF 3GTOF 2R93F 2NVYF 5IP9F 3HOZF 3S1RF 3M3YF 1TWFF 5IPLE 2E2HF 4YFNE 1ZYRE 4XSZE 5IYCF 4Q4ZE 4OIQE 4A3BF 4OIPE 3HOVF 4XLNE 3EQLE 1TWHF 1SMYE 5M3FF 3WODE 3S16F 2BE5E 3S1MF 3K7AF 4A3LF 2NVTF 5C4XF 4BY7F 3S2HF 2O5IE 4KN4E 4C3JF 5C3EF 3GTKF 5TMCE 4OIOE 3CQZF 5IYBF 4Y7NF 2VUMF 2O5JE 2JA8F 3PO3F 1WCMF 2A6EE 5BYHE 1SFOF 2CW0E 3S1NF 2A68E 4JK1E 4AYBK 2JA7F 4A3GF 4A3IF 5E17E 1TWCF 2NVQF 5D4DE 3GTMF 4A3KF 2A6HE 4OINE 1I3QF 4LLGE 3I4NF 3RZDF 5E18E 5M5YF 4BY1F 4A3MF 4MQ9E 2E2IF 4LK0E 3RZOF 3PO2F 4G7HE 4Q5SE 5IYDF 1R9TF 3GTQF 4OIRE 1K83F 2E2JF 4A3CF 4C3IF 4YFKE 4YG2E 5TMFE 4A3DF 1IW7E 5M5XF 3M4OF 4X6AF 5D4EE 2NVXF 2WB1I 3HOWF 4A93F 4C2MF 3GTLF 3HKZK 4G7OE 1TWGF 4Y52F 4YFXE 1QKLA 4XSXE 5M5WF 5D4CE 4A3FF 4A3EF 3S17F 2R92F 3S15F 1HQME 2PPBE 5M3MF 1Y1WF 4GZYE 2YU9F 3HOYF 2Y0SI 4XLPE 1I50F 4MEXE 2A69E 1TWAF 3GTJF 4C3HF 3H3VG 1Y1VF 3DXJE 3H0GF 4A3JF 3S14F 2KRXA 4QIWK 4G7ZE 5FJ8F 1YNJK 4BBSF 5C44F 5IP7F 2PMZK 3S2DF 2JA5F 3FKIF 2B63F
chains in the Genus database with same CATH homology


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