NDB ID: NA0031 PDB ID: 3HOV 
Title:
COMPLETE RNA POLYMERASE II ELONGATION COMPLEX II
Molecular Description:
RNA polymerase II (E.C.2.7.7.6)/DNA/RNA
Deposited:
2009-06-03
Released:
2009-07-28
Structural Keywords:
RH DOUBLE HELIX, OVERHANGING BASES, NICKED
Nucleic Acid Sequence:
Click to show/hide 3 nucleic acid sequences
Chain T
(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DG)(DT)(DT)(DA)(DT)(DG)(DC)(DC)(BRU) (DG)(DG)(DT)
(DC)(DA)(DT)(DT)
Chain P
UGCAUUUCGACCAGGCA
Chain N
(DT)(DA)(DC)(DT)(DA)(DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)
Protein Sequence:
Click to show/hide 12 protein sequences
Chain K
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKN
ACNSIINKLGALKTNFETEWNLQTLAADDAF
Chain J
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD
Chain L
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
Chain A
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGH FGHIDLAKP
VFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQ LVSRGGCGNTQPTIRKDG
LKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP VPPPPVRPSISFNESQRGEDDLTFKLA
DILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGR PVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGD
PNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHP GAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFN
RQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKL
TLRDTFIELDQVLNMLYWVPDWDGVI PTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVG
SSNGGLIHVVTREKGPQ VCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE
SFEDNVVR FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFV
ENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEK QSLDTIGGS
DAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI RRIIQNAQQTFHIDHTKP
SDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQ AFDWVLSNIEAQFLRSVVHPGEMVGVL
AAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYL EPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDP
DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRP
KSLDAETEAEEDHMLKKIENTMLENITLRGVENIE RVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFID
IMEVLGIEAGRAALYKEVYNVIASDG SYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG
VSENVILGQMAPIGTGA FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYG
GADYGEAT SPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP
TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP SYSPTSPSY
SPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR
Chain C
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL EYSRDCFCE
DHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK KGIAKEHAKWGPAAAIEF
EYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV DQVVVRGIDTLQKKVASILLALTQMDQ
DKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW
Chain B
MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE SDNISRKYE
ISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDS ESGKVFIGRLPIMLRSKN
CYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI RSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVED GFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDIL
QKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDH FGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMK
LAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSE WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKE
LKIFTDAGRVYRPLFIV EDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEP
AEANEEND LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ
KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT NTLRMKHGT
YDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG LKFVKVRVRTTKIPQIGD
KFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN EGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASD
AFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA KLLFQELMAMNITPRLYTDRSRDF
Chain E
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVG
VKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRI
QRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Chain D
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK HLKHENAND
ETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV GAVIQLLKSTGLHPFEVA
QLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Chain G
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDG
TVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI
Chain F
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYE
RARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Chain I
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQ
QRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS
Chain H
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSL
ADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR
Primary Citation:
Sydow, J.F., Brueckner, F., Cheung, A.C.M., Damsma, G.E., Dengl, S., Lehmann, E., Vassylyev, D., Cramer, P.
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. 
Mol.Cell, 34, pp. 710 - 721, 2009.
Experimental Information:
X-RAY DIFFRACTION
Space Group:
C 2 2 21
Cell Constants:
a = 222.252 b = 393.383 c = 283.091 (Ångstroms)
α = 90.0 β = 90.0 γ = 90.0 (degrees)
Refinement:
The structure was refined using the CNS program.
The R value is 0.0 for 155150 reflections in
the resolution range 50.0 to 3.5 Ångstroms
with Fobs > 0.0 sigma(Fobs) and with I > 0.0 sigma(I)