Structure of PDB 8to6 Chain J Binding Site BS02

Receptor Information
>8to6 Chain J (length=1335) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQ
CGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR
DCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVA
KTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQ
EQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEK
QVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLH
EQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAI
GVIAAQSIGEPGTQLSSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTEL
KLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVS
GFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVD
AQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQTGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMI
PKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDV
YRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANR
ELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGK
RDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA
Ligand information
>8to6 Chain P (length=42) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cttagtacaccgccagaggtaaaatagtcaacacgcacggtg
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8to6 Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		Y795 Q1326
Binding residue
(residue number reindexed from 1)		Y780 Q1286
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8to6, PDBe:8to6, PDBj:8to6
PDBsum8to6
PubMed38951624
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]