Structure of PDB 8hyj Chain B

Receptor sequence
>8hyjB (length=1054) Species: 3702 (Arabidopsis thaliana) [Search protein sequence]
NLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSF
GEMLVEPSWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMTYSAR
IKVNVQVEVFDILIGSIPVMVKSILCKTSEKGKENCKKGDCAFDQGGYFV
IKGAEKVFIAQEQMCTKRLWISNSPWTVSFRSENKRNRFIVRLSENEKAE
DYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITN
SLIASIHVADAVCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLF
PGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLER
EIRVHLAHARRKMTRAMQKHLSGKPIEHYLDASVITNGLSRAFSTGAWSH
PFRKMERVSGVVANLGRANPLQTLIDLRRTRQQVDARYPHPSHWGRVCFL
STPDGENCGLVKNMSLLGLVSTQSLESVVEKLFACGMEELMDDTCTPLFG
KHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRI
FTDAGRLLRPLLVVENLQKLKQEQYPFDHLLDHGILELIGIEEEEDCNTA
WGIKQLLKEPKIYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKHC
QQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAI
VAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDVQFGKTHVDS
LEDDGFPFIGANMSTGDIVIGRCHSIKLKHTERGIVQKVVLSSNDEGKNF
AAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVIN
PHAFPSRQTPGQLLEAALSKGIACPIQYTKLTRHATPFSTPGVTEITEQL
HRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTG
PVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQ
MHICRKCKTYANGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGITLNF
DTKL
3D structure
PDB8hyj A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex.
ChainB
Resolution4.3 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
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 B R240 K244 F344 R420 R181 K185 F285 R361
BS02 dna B A1065 I1073 K1074 M1078 A961 I969 K970 M974
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0030422 siRNA processing
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0050776 regulation of immune response
GO:0050832 defense response to fungus
GO:0080188 gene silencing by siRNA-directed DNA methylation
GO:0141007 siRNA-mediated retrotransposon silencing by heterochromatin formation
Cellular Component
GO:0000418 RNA polymerase IV complex
GO:0000419 RNA polymerase V complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0030880 RNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8hyj, PDBe:8hyj, PDBj:8hyj
PDBsum8hyj
PubMed37253723
UniProtQ9LK40|NRPD2_ARATH DNA-directed RNA polymerases IV and V subunit 2 (Gene Name=NRPD2)

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