eF-site ID 3gtg-ABCEFHIJKLNRT
PDB Code 3gtg
Chain A, B, C, E, F, H, I, J, K, L, N, R, T
Title Backtracked RNA polymerase II complex with 12mer RNA
Classification TRANSCRIPTION, TRANSFERASE/DNA/RNA HYBRID
Compound DNA-directed RNA polymerase II subunit RPB1
Source ORGANISM_COMMON: yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae;
Sequence A:  GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMD
ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG
HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM
RQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLV
SRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVL
STEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVP
PPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHN
GAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPV
KSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELD
QVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA
KYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPV
LFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADF
DGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG
IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPT
PAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKD
NGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVC
AKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITET
IAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFL
NEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMS
ACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVEN
SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV
KALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQS
LDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGD
LKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRR
IIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRG
KNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAF
DWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLN
TFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEP
GHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTV
IPEDEEIIQLHFSLLDEQQSPWLLRLELDRAAMNDKDLTM
GQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLD
AETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDR
KVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYT
NSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMA
LLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL
FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEES
LV
B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL
QDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTK
PMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFIG
RLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGS
EKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGS
RFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRA
LGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRE
TALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLE
GFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDL
AGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAI
NAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTY
SSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQS
PDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVS
MIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVR
KGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYID
AEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHH
ATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMG
KQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKF
RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSL
FFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLD
DDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENG
IVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQK
GTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLI
ECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARA
RGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFL
KERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDN
KIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
C:  SEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEI
PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLE
YSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIV
SNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKK
GIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEW
PQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVD
QVVVRGIDTLQKKVASILLALTQMDQDKVNF
E:  MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLE
DFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV
EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE
KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIR
KSETSGRYASYRICM
F:  EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVD
LEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEE
LIVDL
H:  MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTL
DINVELFPVAAQDSLTVTIASSLSATRSWRPPQAGDRSLA
DDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYR
NLNNLKQENAYLLIRR
I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP
LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR
ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNP
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTL
L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL
VQFEAR
N:  CTGCTTATCGGTAG
R:  AUCGAGAGGAUG
T:  CTACCGATAAGCAGACGATCCTCTCGAT
Description


Functional site

1) chain A
residue 107
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1734
source : AC1

2) chain A
residue 110
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1734
source : AC1

3) chain A
residue 148
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1734
source : AC1

4) chain A
residue 167
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1734
source : AC1

5) chain A
residue 67
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1735
source : AC2

6) chain A
residue 68
type
sequence Q
description BINDING SITE FOR RESIDUE ZN A 1735
source : AC2

7) chain A
residue 70
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1735
source : AC2

8) chain A
residue 77
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1735
source : AC2

9) chain A
residue 80
type
sequence H
description BINDING SITE FOR RESIDUE ZN A 1735
source : AC2

10) chain B
residue 1163
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 1307
source : AC3

11) chain B
residue 1166
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 1307
source : AC3

12) chain B
residue 1182
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 1307
source : AC3

13) chain B
residue 1185
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 1307
source : AC3

14) chain C
residue 86
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 319
source : AC4

15) chain C
residue 88
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 319
source : AC4

16) chain C
residue 92
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 319
source : AC4

17) chain C
residue 95
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 319
source : AC4

18) chain I
residue 7
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 203
source : AC5

19) chain I
residue 10
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 203
source : AC5

20) chain I
residue 29
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 203
source : AC5

21) chain I
residue 32
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 203
source : AC5

22) chain I
residue 75
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 204
source : AC6

23) chain I
residue 78
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 204
source : AC6

24) chain I
residue 103
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 204
source : AC6

25) chain I
residue 106
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 204
source : AC6

26) chain J
residue 7
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 101
source : AC7

27) chain J
residue 9
type
sequence S
description BINDING SITE FOR RESIDUE ZN J 101
source : AC7

28) chain J
residue 10
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 101
source : AC7

29) chain J
residue 45
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 101
source : AC7

30) chain J
residue 46
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 101
source : AC7

31) chain L
residue 31
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 105
source : AC8

32) chain L
residue 34
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 105
source : AC8

33) chain L
residue 48
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 105
source : AC8

34) chain L
residue 51
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 105
source : AC8

35) chain A
residue 481
type
sequence D
description BINDING SITE FOR RESIDUE MG A 1736
source : AC9

36) chain A
residue 483
type
sequence D
description BINDING SITE FOR RESIDUE MG A 1736
source : AC9

37) chain A
residue 485
type
sequence D
description BINDING SITE FOR RESIDUE MG A 1736
source : AC9

38) chain R
residue 10
type
sequence A
description BINDING SITE FOR RESIDUE MG A 1736
source : AC9

39) chain R
residue 11
type
sequence U
description BINDING SITE FOR RESIDUE MG A 1736
source : AC9

40) chain B
residue 837
type catalytic
sequence D
description 788
source MCSA : MCSA1

41) chain A
residue 483
type catalytic
sequence D
description 788
source MCSA : MCSA1

42) chain A
residue 485
type catalytic
sequence D
description 788
source MCSA : MCSA1

43) chain A
residue 1085
type catalytic
sequence H
description 788
source MCSA : MCSA1

44) 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

45) 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

46) 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

47) 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

48) chain I
residue 40
type MOD_RES
sequence S
description Phosphoserine => ECO:0007744|PubMed:18407956
source Swiss-Prot : SWS_FT_FI5

49) 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

50) 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

51) 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

52) 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

53) 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

54) 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

55) chain I
residue 75-110
type prosite
sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
source prosite : PS00466

56) 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

57) 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

58) 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

59) 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

60) chain B
residue 977-989
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166

61) chain I
residue 7-32
type ZN_FING
sequence CRDCNNMLYPREDKENNRLLFECRTC
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

62) chain A
residue 483
type ZN_FING
sequence D
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

63) chain A
residue 485
type ZN_FING
sequence D
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

64) chain C
residue 88
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

65) chain C
residue 92
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

66) chain C
residue 95
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

67) chain A
residue 107
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

68) chain A
residue 110
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

69) chain A
residue 148
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

70) chain A
residue 167
type ZN_FING
sequence C
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

71) chain A
residue 481
type ZN_FING
sequence D
description C4-type => ECO:0000255
source Swiss-Prot : SWS_FT_FI1

72) chain I
residue 71-111
type ZN_FING
sequence SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
T
description TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
source Swiss-Prot : SWS_FT_FI2

73) chain B
residue 1163
type ZN_FING
sequence C
description TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
source Swiss-Prot : SWS_FT_FI2

74) chain B
residue 1166
type ZN_FING
sequence C
description TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
source Swiss-Prot : SWS_FT_FI2

75) chain B
residue 1182
type ZN_FING
sequence C
description TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
source Swiss-Prot : SWS_FT_FI2

76) chain B
residue 1185
type ZN_FING
sequence C
description TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
source Swiss-Prot : SWS_FT_FI2


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