Structure of PDB 8w8p Chain F

Receptor sequence

>8w8pF (length=346) Species: 300852 (Thermus thermophilus HB8)

SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLI
REVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIA
REGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF
EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ
LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDS
FYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID
GREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

3D structure

• PDB: 8w8p Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
• Chain: F
• Resolution: 3.165 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	F	I321 G322 F332	I244 G245 F255
BS02	dna	F	D79 V81 R82 L85 H86 G89 L93 N191 R193 L194 S197 K200 F209 K226 F227 E228 R231 F233 K234 S236 T237 Y238 T240 W241	D2 V4 R5 L8 H9 G12 L16 N114 R116 L117 S120 K123 F132 K149 F150 E151 R154 F156 K157 S159 T160 Y161 T163 W164
BS03	MG	F	A292 G296 W299	A215 G219 W222

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0016987 sigma factor activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006352 DNA-templated transcription initiation
• GO:0006355 regulation of DNA-templated transcription
• GO:0010468 regulation of gene expression
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:8w8p, PDBe:8w8p, PDBj:8w8p
• PDBsum: 8w8p
• PubMed: 38990947
• UniProt: Q5SKW1