RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with AMPCPP

DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

Structural basis of initial RNA polymerase II transcription.

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4

5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP* TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'

RNA POLYMERASE II SUBUNIT 1, RNA POLYMERASE II SUBUNIT B1, DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT, RPB1, RNA POLYMERASE II SUBUNIT B220

RNA POLYMERASE II SUBUNIT 2, B150, RPB2, DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE

RNA POLYMERASE II SUBUNIT 3, RNA POLYMERASE II SUBUNIT B3, B44.5, DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE, RPB3

RNA POLYMERASE II SUBUNIT B4, B32, RPB4, DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE

RNA POLYMERASES I, II, AND III SUBUNIT ABC1, ABC27, DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE, RPB5

RNA POLYMERASES I, II, AND III SUBUNIT ABC2, ABC23, DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE, RPB6

RNA POLYMERASES I, II, AND III SUBUNIT ABC3, ABC14.4, ABC14.5, DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE, RPB8

RNA POLYMERASE II SUBUNIT B9, B12.6, RPB9, DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE, DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9

RNA POLYMERASES I, II, AND III SUBUNIT ABC5, ABC10-BETA, ABC8, DNA-DIRECTED RNA POLYMERASES I, II, AND III 8.3 KDA POLYPEPTIDE, RPB10

RNA POLYMERASE II SUBUNIT B11, B13.6, RPB11, DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE

RNA POLYMERASES I, II, AND III SUBUNIT ABC4, ABC10-ALPHA, RPB12

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGH
FGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQ
LVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP
VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGR
PVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHP
GAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA
DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI
PTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQ
VCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR
FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFV
ENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEK
QSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI
RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQ
AFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYL
EPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA
AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIE
RVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDG
SYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA
FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEAT
SPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP
TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENS

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE
SDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDS
ESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI
RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVED
GFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDH
FGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS
QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE
WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV
EDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND
LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ
KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT
NTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG
LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN
EGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE
GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA
KLLFQELMAMNITPRLYTDRSRDF

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL
EYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK
KGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK
HLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV
GAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV
EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE
KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA
TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK
PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI
GSIKEDYLGAI

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR
PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS
RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(BRU)
(DG)(DG)(DT)(DC)(DA)(DT)(DT)

RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID
COMPLETE RNA POLYMERASE II ELONGATION COMPLEX WITHSUBSTRATE ANALOGUE GMPCPP
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX
RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
CRYSTAL STRUCTURE OF YEAST SUBCOMPLEX OF RPB4 AND RPB7
COMPLETE RNA POLYMERASE II ELONGATION COMPLEX
RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION
RNA POLYMERASE II COMPLEXED WITH UTP AT 2.3 A RESOLUTION
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 2NT DNA-RNA HYBRID
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID
RNA POLYMERASE II BINARY COMPLEX WITH DNA
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 4NT DNA-RNA HYBRID
COMPLETE 12-SUBUNIT RNA POLYMERASE II AT 3.8 A
ALPHA-AMANITIN INHIBITED COMPLETE RNA POLYMERASE II ELONGATION COMPLEX
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE
CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX B
CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX C
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
YEAST RIBONUCLEIC ACID POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY
CRYSTAL STRUCTURE OF YEAST RNA POLYMERASE II COMPLEXED WITHTHE INHIBITOR ALPHA AMANITIN
COMPLETE RNA POLYMERASE II-RNA INHIBITOR COMPLEX
CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX D
CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX A
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 2NT DNA-RNA HYBRID AND SOAKED WITH GMPCPP

SHEET
DETERMINATION METHOD: DSSP
THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY
A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE SHEETS PRESENTED AS "BP" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY
A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY
A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG BRU APC. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31808. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=51. NUMBER TREATED BY BAD NON- BONDED CONTACTS=9.