eF-site ID 5vvr-ABCDEFGHIJKLMNRT
PDB Code 5vvr
Chain A, B, C, D, E, F, G, H, I, J, K, L, M, N, R, T
Title Ternary complex of RNA Pol II, transcription scaffold and Rad26
Classification TRANSCRIPTION/RNA/DNA
Compound DNA-directed RNA polymerase II subunit RPB1
Source ORGANISM_COMMON: Baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae (strain ATCC 204508 / S288c);
Sequence A:  SAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTR
AKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLA
KPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALA
IKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGC
GNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEI
LNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVR
PSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHH
AIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRA
RLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVP
KSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIR
DSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQ
PSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEM
NLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDT
LCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIK
PKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLI
IDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFG
NIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAK
KKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARD
KAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ
QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRG
LTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED
IMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIG
GSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQV
LLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNA
QQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEII
QNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLS
NIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFA
GVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAAD
QEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDE
EIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDL
TMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKS
LDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKY
DRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRI
YTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRH
MALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVE
ILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDE
ESLVKYMP
B:  FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDY
TLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYV
TKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY
EAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSK
NCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK
LYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEI
LEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRR
GTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFF
LGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF
KTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGL
KYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRR
TNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVK
NLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDA
TRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIR
DIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGH
IAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEE
EESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATT
FTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA
MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL
PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFR
SYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDG
LIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDA
STPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG
DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK
LLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRH
MVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDC
MIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNH
NQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDRSRDF
C:  MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAE
IPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL
EYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK
KGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKE
WPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKV
D:  STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGE
EEELIALNLSEARLVIKEALVERRRAFKRSETREKELESI
DVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQL
LKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDE
LERILKELSNLETLY
E:  MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLE
DFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV
EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE
KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIR
KSETSGRYASYRICM
F:  PKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGE
TDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVD
L
G:  MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTG
KFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK
PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI
GSIKEDYLGAI
H:  MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTL
DINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR
PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR
I:  MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS
PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS
RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNPLEKRD
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNL
L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL
VQFEAR
M:  LRFRGQPGEAKDDGDELYYQERLKKWVKQRSCGSQRSSDL
PEWRRPHPNIPDAKLNSQFKIPGEIYSLLFNYQKTCVQWL
YELYQQNCGGIIGDEMGLGKTIQVIAFIAALHHSGLLTGP
VLIVCPATVMKQWCNEFQHWWPPLRTVILHSMGSGMASDQ
HILITTYVGLRIHSDKLLKVKWQYAVLDEGHKIRNPDSEI
SLTCKKLKTHNRIILSGTPIQNNLTELWSLFDFIFPGKLG
TLPVFQQQFVIPINIGGYANATNIQVQTGYKCAVALRDLI
SPYLLRRVKADVAKDLPQKKEMVLFCKLTKYQRSKYLEFL
HSSDLNQIQNGKRNVLFGIDILRKICNHPDGDPKRSGKMQ
VVKQLLLLWHKQGYKALLFTQSRQMLDILEEFISTKDPDL
SHLNYLRMDGTTNIKGRQSLVDRFNNESFDVFLLTTRVGG
LGVNLTGANRIIIFDPDWNPSTDMQARERAWRIGQKREVS
IYRLMVGGSIEEKIYHRQIFKQF
N:  CTAGTTGATCTCATATTTCATTCCTACTCAGGAGAAGGAG
CAGAGCG
R:  AUCGAGAGGA
T:  CGCTCTGCTCCTTCTCCCATCCTCTCGATGGCTATGAGAT
CAACTAG
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 165
type
sequence G
description binding site for residue ZN A 1801
source : AC1
5) chain A
residue 166
type
sequence G
description binding site for residue ZN A 1801
source : AC1
6) chain A
residue 167
type
sequence C
description binding site for residue ZN A 1801
source : AC1
7) chain A
residue 67
type
sequence C
description binding site for residue ZN A 1802
source : AC2
8) chain A
residue 70
type
sequence C
description binding site for residue ZN A 1802
source : AC2
9) chain A
residue 77
type
sequence C
description binding site for residue ZN A 1802
source : AC2
10) chain A
residue 78
type
sequence P
description binding site for residue ZN A 1802
source : AC2
11) chain A
residue 80
type
sequence H
description binding site for residue ZN A 1802
source : AC2
12) chain A
residue 446
type
sequence R
description binding site for residue MG A 1803
source : AC3
13) chain B
residue 1163
type
sequence C
description binding site for residue ZN B 1301
source : AC4
14) chain B
residue 1166
type
sequence C
description binding site for residue ZN B 1301
source : AC4
15) chain B
residue 1185
type
sequence C
description binding site for residue ZN B 1301
source : AC4
16) chain C
residue 81
type
sequence E
description binding site for residue ZN C 401
source : AC5
17) chain C
residue 86
type
sequence C
description binding site for residue ZN C 401
source : AC5
18) chain C
residue 88
type
sequence C
description binding site for residue ZN C 401
source : AC5
19) chain C
residue 92
type
sequence C
description binding site for residue ZN C 401
source : AC5
20) chain C
residue 95
type
sequence C
description binding site for residue ZN C 401
source : AC5
21) chain I
residue 7
type
sequence C
description binding site for residue ZN I 201
source : AC6
22) chain I
residue 10
type
sequence C
description binding site for residue ZN I 201
source : AC6
23) chain I
residue 12
type
sequence N
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 78
type
sequence C
description binding site for residue ZN I 202
source : AC7
27) chain I
residue 103
type
sequence C
description binding site for residue ZN I 202
source : AC7
28) chain I
residue 106
type
sequence C
description binding site for residue ZN I 202
source : AC7
29) chain I
residue 108
type
sequence H
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 43
type
sequence R
description binding site for residue ZN J 101
source : AC8
33) chain J
residue 45
type
sequence C
description binding site for residue ZN J 101
source : AC8
34) chain J
residue 46
type
sequence C
description binding site for residue ZN J 101
source : AC8
35) chain L
residue 31
type
sequence C
description binding site for residue ZN L 101
source : AC9
36) chain L
residue 34
type
sequence C
description binding site for residue ZN L 101
source : AC9
37) chain L
residue 50
type
sequence D
description binding site for residue ZN L 101
source : AC9
38) chain L
residue 51
type
sequence C
description binding site for residue ZN L 101
source : AC9
39) chain B
residue 837
type catalytic
sequence D
description 788
source MCSA : MCSA1
40) chain A
residue 483
type catalytic
sequence D
description 788
source MCSA : MCSA1
41) chain A
residue 485
type catalytic
sequence D
description 788
source MCSA : MCSA1
42) chain A
residue 1085
type catalytic
sequence H
description 788
source MCSA : MCSA1
43) 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
44) 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
45) 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
46) 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
47) 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
48) 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
49) 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
50) 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
51) chain M
residue 322
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
52) chain A
residue 483
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
53) chain A
residue 485
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
54) chain J
residue 10
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
55) chain J
residue 45
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
56) chain J
residue 46
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
57) chain A
residue 107
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
58) chain A
residue 110
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
59) chain A
residue 148
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
60) chain A
residue 167
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
61) chain A
residue 481
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00541
source Swiss-Prot : SWS_FT_FI1
62) 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
63) 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
64) chain I
residue 75-110
type prosite
sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
source prosite : PS00466
65) 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
66) 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
67) 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
68) 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
69) chain B
residue 977-989
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166
70) chain L
residue 34
type MOD_RES
sequence C
description Phosphoserine => ECO:0007744|PubMed:19779198
source Swiss-Prot : SWS_FT_FI2
71) chain L
residue 48
type MOD_RES
sequence C
description Phosphoserine => ECO:0007744|PubMed:19779198
source Swiss-Prot : SWS_FT_FI2
72) chain L
residue 51
type MOD_RES
sequence C
description Phosphoserine => ECO:0007744|PubMed:19779198
source Swiss-Prot : SWS_FT_FI2
73) chain B
residue 1185
type MOD_RES
sequence C
description Phosphoserine => ECO:0007744|PubMed:19779198
source Swiss-Prot : SWS_FT_FI2
74) 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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