eF-site ID 6rip-ABCDENRT
PDB Code 6rip
Chain A, B, C, D, E, N, R, T
Title Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex in swiveled state
Classification TRANSCRIPTION
Compound Non-template DNA
Source (6RIP)
Sequence A:  EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRI
LLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLK
GLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKP
QHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDER
PIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEME
TNGTIDPEEAIRRAATILAEQLEAFVDL
B:  SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNAL
RRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILL
NLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEI
VKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEE
DERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVI
EMETNGTIDPEEAIRRAATILAEQLEAFV
C:  VYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQ
DPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFD
VQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQE
VYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDK
GKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRR
RKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMEL
VPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDD
VKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDL
LAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLS
ALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVG
RMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGE
VDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSL
GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPL
SEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI
ETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTD
EIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGE
SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALM
GANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG
GVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQ
NTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR
VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSR
DTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD
ILVGKVTPKVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDK
RALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGG
VEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKH
EFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPG
DKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGV
PSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLRE
FIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIA
TPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFER
PVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKA
QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTK
MYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
D:  EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDG
LFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQT
KVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDI
ERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDE
FDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPL
DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNE
KRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ
GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALE
LFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCA
AYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN
GEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAER
LYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVG
RAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIIS
EAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSK
AMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAA
QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFIS
THGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTAD
ILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVC
AHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTF
SSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDE
FGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPV
ITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAER
TAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIV
QLEDGVQISSGDTLARITGGLPRVADLFEARRPKEPAILA
EISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLN
VFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEV
QDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEG
EQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATE
SFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLI
PAGTGYAYHQDRMRRR
E:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE
ENDKTTVIALREIEEGLINNQILDVRERQEQQE
N:  ACCCATTCAGGCATGGCTAGCTGC
R:  UCAGGCGAUGUUU
T:  GCAGCTAGCCATGCACATCGCCTGGAATGGGT
Description (1)  DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega/DNA Complex


Functional site

1) chain D
residue 70
type
sequence C
description binding site for residue ZN D 1501
source : AC1

2) chain D
residue 71
type
sequence L
description binding site for residue ZN D 1501
source : AC1

3) chain D
residue 72
type
sequence C
description binding site for residue ZN D 1501
source : AC1

4) chain D
residue 85
type
sequence C
description binding site for residue ZN D 1501
source : AC1

5) chain D
residue 88
type
sequence C
description binding site for residue ZN D 1501
source : AC1

6) chain D
residue 814
type
sequence C
description binding site for residue ZN D 1502
source : AC2

7) chain D
residue 883
type
sequence R
description binding site for residue ZN D 1502
source : AC2

8) chain D
residue 888
type
sequence C
description binding site for residue ZN D 1502
source : AC2

9) chain D
residue 895
type
sequence C
description binding site for residue ZN D 1502
source : AC2

10) chain D
residue 898
type
sequence C
description binding site for residue ZN D 1502
source : AC2

11) chain D
residue 460
type
sequence D
description binding site for residue MG D 1503
source : AC3

12) chain D
residue 462
type
sequence D
description binding site for residue MG D 1503
source : AC3

13) chain D
residue 464
type
sequence D
description binding site for residue MG D 1503
source : AC3

14) chain R
residue 10
type
sequence G
description binding site for residue MG D 1503
source : AC3

15) chain R
residue 11
type
sequence U
description binding site for residue MG D 1503
source : AC3

16) chain D
residue 983
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000255|HAMAP-Rule:MF_01322, ECO:0000269|PubMed:18723842
source Swiss-Prot : SWS_FT_FI2

17) chain C
residue 1063-1075
type prosite
sequence GDKMAGRHGNKGV
description RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV
source prosite : PS01166

18) chain D
residue 70
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

19) chain D
residue 895
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

20) chain D
residue 898
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

21) chain D
residue 72
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

22) chain D
residue 85
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

23) chain D
residue 88
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

24) chain D
residue 460
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

25) chain D
residue 462
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

26) chain D
residue 464
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

27) chain D
residue 814
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1

28) chain D
residue 888
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:32871103, ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY
source Swiss-Prot : SWS_FT_FI1


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