eF-site ID 6bqf-ABCEFHIJKLRT
PDB Code 6bqf
Chain A, B, C, E, F, H, I, J, K, L, R, T
Title Pol II elongation complex with 'dT-AP' at i+1, i-1 position
Classification TRANSFERASE/TRANSCRIPTION
Compound DNA-directed RNA polymerase II subunit RPB1
Source (6BQF)
Sequence A:  GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMD
ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG
HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM
RQALAIKDSKKRFAAIWTLCKTKMVCGGCGNTQPTIRKDG
LKLVGSWVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEW
MILTCLPVPPPPVRPSIEDDLTFKLADILKANISLETLEH
NGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRP
VKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL
DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG
AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDP
VLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD
FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCM
GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP
TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK
DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQV
CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITE
TIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF
LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQM
SACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE
NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL
VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ
SLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILG
DLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR
RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR
GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA
FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTK
VTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKL
IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLH
FSQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDL
FVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLR
GVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLS
EVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYN
VIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNT
GALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMA
PIGTGAFDVMID
B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL
QDIICEDSTLIEISFGKIYVTKPMVNESDGVTHALYPQEA
RLRNLTYSSGLFVDVKKKVFIGRLPIMLRSKNCYLSEATE
SDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVF
KKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATL
PYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEM
LKPCVEDGFVIQDRETALDFIGRRGKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRD
HFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTLAIN
AKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYS
STLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGL
VKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSP
DATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSM
IRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRK
GHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIA
MQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAA
SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMA
NILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGY
NQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITET
FEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIG
KTTPITAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKF
VKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA
EGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGD
ASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMA
QIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS
RDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHIC
GICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL
FQELMAMNITPRLYTDR
C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP
TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY
SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS
NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG
IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP
QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ
VVVRGIDTLQKKVASILLALTQMDQD
E:  QENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDF
KAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEF
CDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK
LVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKR
ELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKS
ETSGRYASYRICM
F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL
EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL
IVDL
H:  NTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDI
NVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDYD
YVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYLNNLK
QENAYLLIRR
I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP
LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR
ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKN
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNP
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTL
L:  LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQ
FEAR
R:  AUCGAGAGA
T:  CTXCTCTCGATG
Description


Functional site
1) chain A
residue 107
type
sequence C
description binding site for residue ZN A 1801
source : AC1
2) chain A
residue 108
type
sequence M
description binding site for residue ZN A 1801
source : AC1
3) chain A
residue 110
type
sequence C
description binding site for residue ZN A 1801
source : AC1
4) chain A
residue 148
type
sequence C
description binding site for residue ZN A 1801
source : AC1
5) chain A
residue 167
type
sequence C
description binding site for residue ZN A 1801
source : AC1
6) chain A
residue 67
type
sequence C
description binding site for residue ZN A 1802
source : AC2
7) chain A
residue 70
type
sequence C
description binding site for residue ZN A 1802
source : AC2
8) chain A
residue 77
type
sequence C
description binding site for residue ZN A 1802
source : AC2
9) chain A
residue 80
type
sequence H
description binding site for residue ZN A 1802
source : AC2
10) chain A
residue 481
type
sequence D
description binding site for residue MG A 1803
source : AC3
11) chain A
residue 483
type
sequence D
description binding site for residue MG A 1803
source : AC3
12) chain A
residue 485
type
sequence D
description binding site for residue MG A 1803
source : AC3
13) chain R
residue 9
type
sequence A
description binding site for residue MG A 1803
source : AC3
14) chain B
residue 1163
type
sequence C
description binding site for residue ZN B 1301
source : AC4
15) chain B
residue 1166
type
sequence C
description binding site for residue ZN B 1301
source : AC4
16) chain B
residue 1182
type
sequence C
description binding site for residue ZN B 1301
source : AC4
17) chain B
residue 1185
type
sequence C
description binding site for residue ZN B 1301
source : AC4
18) chain C
residue 86
type
sequence C
description binding site for residue ZN C 401
source : AC5
19) chain C
residue 88
type
sequence C
description binding site for residue ZN C 401
source : AC5
20) chain C
residue 92
type
sequence C
description binding site for residue ZN C 401
source : AC5
21) chain C
residue 95
type
sequence C
description binding site for residue ZN C 401
source : AC5
22) chain I
residue 7
type
sequence C
description binding site for residue ZN I 201
source : AC6
23) chain I
residue 10
type
sequence C
description binding site for residue ZN I 201
source : AC6
24) chain I
residue 29
type
sequence C
description binding site for residue ZN I 201
source : AC6
25) chain I
residue 32
type
sequence C
description binding site for residue ZN I 201
source : AC6
26) chain I
residue 75
type
sequence C
description binding site for residue ZN I 202
source : AC7
27) chain I
residue 78
type
sequence C
description binding site for residue ZN I 202
source : AC7
28) chain I
residue 103
type
sequence C
description binding site for residue ZN I 202
source : AC7
29) chain I
residue 106
type
sequence C
description binding site for residue ZN I 202
source : AC7
30) chain J
residue 7
type
sequence C
description binding site for residue ZN J 101
source : AC8
31) chain J
residue 10
type
sequence C
description binding site for residue ZN J 101
source : AC8
32) chain J
residue 45
type
sequence C
description binding site for residue ZN J 101
source : AC8
33) chain J
residue 46
type
sequence C
description binding site for residue ZN J 101
source : AC8
34) chain L
residue 31
type
sequence C
description binding site for residue ZN L 101
source : AC9
35) chain L
residue 34
type
sequence C
description binding site for residue ZN L 101
source : AC9
36) chain L
residue 48
type
sequence C
description binding site for residue ZN L 101
source : AC9
37) chain L
residue 51
type
sequence C
description binding site for residue ZN L 101
source : AC9
38) 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
39) 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
40) 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
41) 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
42) 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
43) chain B
residue 977-989
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166
44) 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
45) 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
46) 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
47) 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
48) chain I
residue 75-110
type prosite
sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
source prosite : PS00466
49) 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
50) chain B
residue 837
type catalytic
sequence D
description 788
source MCSA : MCSA1
51) chain A
residue 483
type catalytic
sequence D
description 788
source MCSA : MCSA1
52) chain A
residue 485
type catalytic
sequence D
description 788
source MCSA : MCSA1
53) chain A
residue 483
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
54) chain A
residue 485
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
55) chain A
residue 107
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
56) chain A
residue 110
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
57) chain A
residue 148
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
58) chain A
residue 167
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
59) chain A
residue 481
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
60) chain J
residue 10
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
61) chain J
residue 45
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
62) chain J
residue 46
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
63) chain L
residue 31-51
type ZN_FING
sequence CAECSSKLSLSRTDAVRCKDC
description C4-type
source Swiss-Prot : SWS_FT_FI1
64) chain B
residue 1185
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
65) chain L
residue 31
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
66) chain L
residue 34
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
67) chain L
residue 48
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
68) chain L
residue 51
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
69) 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
70) 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
71) 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
72) 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
73) chain I
residue 40
type MOD_RES
sequence S
description Phosphoserine => ECO:0007744|PubMed:18407956
source Swiss-Prot : SWS_FT_FI5

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