Structure of PDB 8w8o Chain D

Receptor sequence

>8w8oD (length=1481) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILVPVEKRQLLT
DEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVAL
YRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAE
EEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPL
AEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVV
VPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFE
DDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDA
RMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLD
SGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRL
KKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLT
DILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFK
PFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNR
APTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSF
AQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGL
EFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVA
HGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDV
PQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDA
VIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVT
QAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFE
VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHE
IVVREADCGTTNYISVPLFQPDVTRSLRLRKRADIEAGLYGRVLAREVEV
LGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCY
GYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTQGLPRVIELFEARRPKAK
AVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEA
GQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIV
VRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLL
MGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRL
IPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

3D structure

• PDB: 8w8o Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
• Chain: D
• Resolution: 2.512 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	D	R586 K610 R615 R622 A705 T1088 A1089 Y1093	R582 K606 R611 R618 A701 T1084 A1085 Y1089
BS02	dna	D	P109 R1266	P107 R1245
BS03	rna	D	R704 D741 D743	R700 D737 D739
BS04	ZN	D	C1112 C1194 C1201 C1204	C1108 C1189 C1196 C1199
BS05	ZN	D	C58 C73 C76	C56 C71 C74
BS06	MG	D	D739 D741 D743	D735 D737 D739
BS07	MG	D	W897 E898 I900	W893 E894 I896

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

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:8w8o, PDBe:8w8o, PDBj:8w8o
• PDBsum: 8w8o
• PubMed: 38990947
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)