eF-site ID 5c44-ABCDEFGHIJKLRSU
PDB Code 5c44
Chain A, B, C, D, E, F, G, H, I, J, K, L, R, S, U
Title Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble
Classification TRANSFERASE/DNA/RNA
Compound DNA-directed RNA polymerase II subunit RPB1
Source ORGANISM_COMMON: Baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae (strain ATCC 204508 / S288c);
Sequence A:  VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETM
DETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHF
GHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL
MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQL
VSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRV
LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPV
PPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEH
NGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRP
VKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL
DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG
AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDP
VLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD
FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCM
GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP
TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK
DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQV
CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITE
TIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF
LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQM
SACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE
NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL
VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ
SLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILG
DLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR
RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR
GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA
FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL
FHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPG
HAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVI
PEDEEIIQLHFSFDQQSPWLLRLELDRAAMNDKDLTMGQV
GERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPAEEDHML
KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVK
EPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLG
IEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDD
CRGVSENVILGQMAPIGTGAFDVMIDEESLVKYM
B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL
QDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTK
PMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEA
IDVPGRELKYELIDSESGKVFIGRLPIMLRSKNCYLSEAT
ESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQV
FKKAAPSPISHVAEIRSALEKGRFISTLQVKLYGRSSART
IATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQ
MLEMLKPCVEDGFVIQDRETALDFIGRLGIRIQYAKDILQ
KEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDD
RDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVE
EAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRA
GVSQVLNRYTYSSTLSHLRRTNTPIGRDGKPRQLHNTHWG
LVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE
WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETL
RTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV
EDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGL
VEYIDAEEEESILIAMQPEDLEPAEAKRIRATTFTHCEIH
PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN
YNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAI
VAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK
KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVR
VSGEDVIIGKTTPISPDEEELGTAYHSKRDASTPLRSTEN
GIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQ
KGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHL
IECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQS
RGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHAR
ARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASF
LKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCD
NKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF
C:  EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPT
LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYS
RDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSN
LMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGI
AKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQ
SKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQV
VVRGIDTLQKKVASILLALTQMDQD
D:  STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGE
EEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKEL
ESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAV
IQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS
DDELERILKELSNLETLY
E:  DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLED
FKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE
FCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM
KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEK
RELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRK
SETSGRYASYRICM
F:  LKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVF
VDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSV
EELIVDL
G:  MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTG
KFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK
PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI
GSIKEDYLGAI
H:  MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTL
DINVELFPVAAQDSLTVTIASSLNATRSWRPPQAGDRSLA
DDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYR
NLNNLQENAYLLIRR
I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP
LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR
ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNP
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTLA
L:  LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQ
FEAR
R:  UCGAGAGGA
S:  TGCTTATCGGTAG
U:  CTACCGATAAGCAGACGATCCTCTCGA
Description (1)  DNA-directed RNA polymerase II /RNA/DNA Complex


Functional site
1) chain F
residue 86-100
type prosite
sequence TKYERARILGTRALQ
description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ
source prosite : PS01111
2) chain L
residue 31-51
type ZN_FING
sequence CAECSSKLSLSRTDAVRCKDC
description C4-type
source Swiss-Prot : SWS_FT_FI1
3) chain A
residue 483
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
4) chain A
residue 485
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
5) chain A
residue 107
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
6) chain A
residue 110
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
7) chain A
residue 148
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
8) chain A
residue 167
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
9) chain A
residue 481
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
10) chain J
residue 45
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
11) chain J
residue 46
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
12) chain J
residue 10
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
13) chain I
residue 7
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI3
14) chain I
residue 10
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI3
15) chain I
residue 29
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI3
16) chain I
residue 32
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI3
17) chain I
residue 75
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI4
18) chain I
residue 78
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI4
19) chain I
residue 103
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI4
20) chain I
residue 106
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
source Swiss-Prot : SWS_FT_FI4
21) chain I
residue 40
type MOD_RES
sequence S
description Phosphoserine => ECO:0007744|PubMed:18407956
source Swiss-Prot : SWS_FT_FI5
22) chain B
residue 977-989
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166
23) chain E
residue 147-160
type prosite
sequence HELVPKHIRLSSDE
description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE
source prosite : PS01110
24) chain J
residue 2-11
type prosite
sequence IVPVRCFSCG
description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG
source prosite : PS01112
25) chain K
residue 35-66
type prosite
sequence FEKEDHTLGNLIRAELLNDRKVLFAAYKVEHP
description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP
source prosite : PS01154
26) chain C
residue 31-71
type prosite
sequence NSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLI
P
description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP
source prosite : PS00446
27) chain I
residue 75-110
type prosite
sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
source prosite : PS00466
28) chain I
residue 6-32
type prosite
sequence FCRDCNNMLYPREDKENNRLLFECRTC
description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCrDCNNMLypredkennrllfeCrtC
source prosite : PS01030
29) chain B
residue 837
type catalytic
sequence D
description 788
source MCSA : MCSA1
30) chain A
residue 483
type catalytic
sequence D
description 788
source MCSA : MCSA1
31) chain A
residue 485
type catalytic
sequence D
description 788
source MCSA : MCSA1
32) chain A
residue 1085
type catalytic
sequence H
description 788
source MCSA : MCSA1
33) chain B
residue 1185
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
34) chain L
residue 51
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
35) chain L
residue 31
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
36) chain L
residue 34
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
37) chain L
residue 48
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2

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