|
eF-site ID
|
5c44-ABCDEFGHIJKL |
PDB Code
|
5c44 |
Chain
|
A, B, C, D, E, F, G, H, I, J, K, L |
|
|
|
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
|
|
Description
|
(1) |
DNA-directed RNA polymerase II /RNA/DNA Complex
|
|
Functional site
|
|
1)
|
chain |
B |
residue |
837 |
type |
catalytic |
sequence |
D
|
description |
788
|
source |
MCSA : MCSA1
|
|
2)
|
chain |
A |
residue |
483 |
type |
catalytic |
sequence |
D
|
description |
788
|
source |
MCSA : MCSA1
|
|
3)
|
chain |
A |
residue |
485 |
type |
catalytic |
sequence |
D
|
description |
788
|
source |
MCSA : MCSA1
|
|
4)
|
chain |
A |
residue |
1085 |
type |
catalytic |
sequence |
H
|
description |
788
|
source |
MCSA : MCSA1
|
|
5)
|
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
|
|
6)
|
chain |
I |
residue |
75-110 |
type |
prosite |
sequence |
CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF
|
description |
ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
|
source |
prosite : PS00466
|
|
7)
|
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
|
|
8)
|
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
|
|
9)
|
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
|
|
10)
|
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
|
|
11)
|
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
|
|
12)
|
chain |
B |
residue |
977-989 |
type |
prosite |
sequence |
GDKFASRHGQKGT
|
description |
RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
|
source |
prosite : PS01166
|
|
13)
|
chain |
L |
residue |
31-51 |
type |
ZN_FING |
sequence |
CAECSSKLSLSRTDAVRCKDC
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
14)
|
chain |
A |
residue |
483 |
type |
ZN_FING |
sequence |
D
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
15)
|
chain |
A |
residue |
485 |
type |
ZN_FING |
sequence |
D
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
16)
|
chain |
J |
residue |
10 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
17)
|
chain |
J |
residue |
45 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
18)
|
chain |
J |
residue |
46 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
19)
|
chain |
A |
residue |
107 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
20)
|
chain |
A |
residue |
110 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
21)
|
chain |
A |
residue |
148 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
22)
|
chain |
A |
residue |
167 |
type |
ZN_FING |
sequence |
C
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
23)
|
chain |
A |
residue |
481 |
type |
ZN_FING |
sequence |
D
|
description |
C4-type
|
source |
Swiss-Prot : SWS_FT_FI1
|
|
24)
|
chain |
L |
residue |
31 |
type |
BINDING |
sequence |
C
|
description |
|
source |
Swiss-Prot : SWS_FT_FI2
|
|
25)
|
chain |
L |
residue |
34 |
type |
BINDING |
sequence |
C
|
description |
|
source |
Swiss-Prot : SWS_FT_FI2
|
|
26)
|
chain |
L |
residue |
48 |
type |
BINDING |
sequence |
C
|
description |
|
source |
Swiss-Prot : SWS_FT_FI2
|
|
27)
|
chain |
L |
residue |
51 |
type |
BINDING |
sequence |
C
|
description |
|
source |
Swiss-Prot : SWS_FT_FI2
|
|
28)
|
chain |
B |
residue |
1185 |
type |
BINDING |
sequence |
C
|
description |
|
source |
Swiss-Prot : SWS_FT_FI2
|
|
29)
|
chain |
I |
residue |
7 |
type |
BINDING |
sequence |
C
|
description |
BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
|
source |
Swiss-Prot : SWS_FT_FI3
|
|
30)
|
chain |
I |
residue |
10 |
type |
BINDING |
sequence |
C
|
description |
BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
|
source |
Swiss-Prot : SWS_FT_FI3
|
|
31)
|
chain |
I |
residue |
29 |
type |
BINDING |
sequence |
C
|
description |
BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
|
source |
Swiss-Prot : SWS_FT_FI3
|
|
32)
|
chain |
I |
residue |
32 |
type |
BINDING |
sequence |
C
|
description |
BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499
|
source |
Swiss-Prot : SWS_FT_FI3
|
|
33)
|
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
|
|
34)
|
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
|
|
35)
|
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
|
|
36)
|
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
|
|
37)
|
chain |
I |
residue |
40 |
type |
MOD_RES |
sequence |
S
|
description |
Phosphoserine => ECO:0007744|PubMed:18407956
|
source |
Swiss-Prot : SWS_FT_FI5
|
|
|
|