eF-site ID 5c4a-ABCDEFGHIJKLRSU
PDB Code 5c4a
Chain A, B, C, D, E, F, G, H, I, J, K, L, R, S, U

click to enlarge
Title Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble
Classification TRANSFERASE/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:  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
KVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAK
LIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQL
HFSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK
NDLFVIWSEDNDEKLIIRCRVVRPAEEDHMLKKIENTMLE
NITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETD
GVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALY
KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGF
NRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVI
LGQMAPIGTGAFDVMIDEESLVKYM
B:  DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTL
QDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTK
PMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKTYEAID
VPGRELKYEDSESGKVFIGRLPIMLRSKNCYLSEATESDL
YKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKA
APSPISHVAEIRSALEKGSRFISTLQVKLYGRSSARTIKA
TLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQML
EMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQY
AKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALD
RKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY
MQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKK
AMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGAKPRQLHN
THWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIIT
FLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARL
METLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRP
LFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLL
NEGLVEYIDAEEEESILIAMQPEDLEPAAKRIRATTFTHC
EIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVF
LTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ
NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMD
QEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP
GVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPL
RSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFA
SRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRM
TVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLRE
HGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDD
KIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAH
GAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFE
CKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS
RD
C:  EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPT
LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYS
RDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSN
LMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGI
AKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQ
SKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQV
VVRGIDTLQKKVASILLALTQMDQD
D:  RLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLS
EARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQT
TGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLH
PFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKE
LSNLETLY
E:  DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLED
FKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE
FCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM
KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEK
RELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRK
SETSGRYASYRICM
F:  LKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVF
VDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSV
EELIVDL
G:  MFFIKDLSLITLHPSFFGPRMKQYLKTKLLEEVEGSCTGK
FGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKP
FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTF
NAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIG
SIKEDYLGAI
H:  MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTL
DINVELFPVAAQDSLTVTIASSLNATRSWRPPQAGDRSLA
DDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYR
NLNNLQENAYLLIRR
I:  TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSP
LVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR
ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNPL
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTLA
L:  LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQ
FEAR
R:  UCGAGAGGA
S:  TGTACTTATCGGTAGG
U:  CCTACCGATAAGTACACGATCCTCTCGAA
Description


Functional site
1) chain A
residue 108
type
sequence M
description binding site for residue ZN A 1801
source : AC1
2) chain A
residue 110
type
sequence C
description binding site for residue ZN A 1801
source : AC1
3) chain A
residue 148
type
sequence C
description binding site for residue ZN A 1801
source : AC1
4) chain A
residue 167
type
sequence C
description binding site for residue ZN A 1801
source : AC1
5) chain A
residue 67
type
sequence C
description binding site for residue ZN A 1802
source : AC2
6) chain A
residue 77
type
sequence C
description binding site for residue ZN A 1802
source : AC2
7) chain A
residue 78
type
sequence P
description binding site for residue ZN A 1802
source : AC2
8) chain A
residue 80
type
sequence H
description binding site for residue ZN A 1802
source : AC2
9) chain A
residue 481
type
sequence D
description binding site for residue MG A 1803
source : AC3
10) chain A
residue 483
type
sequence D
description binding site for residue MG A 1803
source : AC3
11) chain A
residue 485
type
sequence D
description binding site for residue MG A 1803
source : AC3
12) chain R
residue 10
type
sequence A
description binding site for residue MG A 1803
source : AC3
13) chain A
residue 1420
type
sequence D
description binding site for residue MG A 1804
source : AC4
14) chain B
residue 1163
type
sequence C
description binding site for residue ZN B 1301
source : AC5
15) chain B
residue 1166
type
sequence C
description binding site for residue ZN B 1301
source : AC5
16) chain B
residue 1170
type
sequence T
description binding site for residue ZN B 1301
source : AC5
17) chain B
residue 1182
type
sequence C
description binding site for residue ZN B 1301
source : AC5
18) chain B
residue 1185
type
sequence C
description binding site for residue ZN B 1301
source : AC5
19) chain C
residue 86
type
sequence C
description binding site for residue ZN C 401
source : AC6
20) chain C
residue 88
type
sequence C
description binding site for residue ZN C 401
source : AC6
21) chain C
residue 92
type
sequence C
description binding site for residue ZN C 401
source : AC6
22) chain C
residue 95
type
sequence C
description binding site for residue ZN C 401
source : AC6
23) chain I
residue 7
type
sequence C
description binding site for residue ZN I 201
source : AC7
24) chain I
residue 10
type
sequence C
description binding site for residue ZN I 201
source : AC7
25) chain I
residue 29
type
sequence C
description binding site for residue ZN I 201
source : AC7
26) chain I
residue 32
type
sequence C
description binding site for residue ZN I 201
source : AC7
27) chain I
residue 75
type
sequence C
description binding site for residue ZN I 202
source : AC8
28) chain I
residue 78
type
sequence C
description binding site for residue ZN I 202
source : AC8
29) chain I
residue 80
type
sequence S
description binding site for residue ZN I 202
source : AC8
30) chain I
residue 106
type
sequence C
description binding site for residue ZN I 202
source : AC8
31) chain J
residue 7
type
sequence C
description binding site for residue ZN J 101
source : AC9
32) chain J
residue 10
type
sequence C
description binding site for residue ZN J 101
source : AC9
33) chain J
residue 45
type
sequence C
description binding site for residue ZN J 101
source : AC9
34) chain J
residue 46
type
sequence C
description binding site for residue ZN J 101
source : AC9
35) chain L
residue 34
type
sequence C
description binding site for residue ZN L 101
source : AD1
36) chain L
residue 36
type
sequence S
description binding site for residue ZN L 101
source : AD1
37) chain L
residue 48
type
sequence C
description binding site for residue ZN L 101
source : AD1
38) chain L
residue 51
type
sequence C
description binding site for residue ZN L 101
source : AD1
39) chain I
residue 75-110
type prosite
sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
source prosite : PS00466
40) chain B
residue 977-989
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166
41) 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
42) 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
43) 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
44) 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
45) 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
46) 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
47) chain J
residue 45
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
48) chain J
residue 46
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
49) chain A
residue 483
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
50) chain A
residue 485
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
51) chain A
residue 107
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
52) chain A
residue 110
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
53) chain A
residue 148
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
54) chain A
residue 167
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
55) chain A
residue 481
type ZN_FING
sequence D
description C4-type
source Swiss-Prot : SWS_FT_FI1
56) chain L
residue 31-51
type ZN_FING
sequence CAECSSKLSLSRTDAVRCKDC
description C4-type
source Swiss-Prot : SWS_FT_FI1
57) chain J
residue 10
type ZN_FING
sequence C
description C4-type
source Swiss-Prot : SWS_FT_FI1
58) chain L
residue 31
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
59) chain L
residue 34
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
60) chain L
residue 48
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
61) chain L
residue 51
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
62) chain B
residue 1185
type BINDING
sequence C
description
source Swiss-Prot : SWS_FT_FI2
63) chain B
residue 837
type catalytic
sequence D
description 788
source MCSA : MCSA1
64) chain A
residue 483
type catalytic
sequence D
description 788
source MCSA : MCSA1
65) chain A
residue 485
type catalytic
sequence D
description 788
source MCSA : MCSA1
66) chain I
residue 40
type MOD_RES
sequence S
description Phosphoserine => ECO:0007744|PubMed:18407956
source Swiss-Prot : SWS_FT_FI5
67) 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
68) 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
69) 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
70) 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
71) 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
72) 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
73) 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
74) 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

Display surface

Download
Links