Structure of PDB 8xme Chain B

Receptor sequence
>8xmeB (length=1061) Species: 3702 (Arabidopsis thaliana) [Search protein sequence]
NLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSF
GEMLVEPSWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMTYSAR
IKVNVQVEVFDILIGSIPVMVKSILCKTSEKGKENCKKGDCAFDQGGYFV
IKGAEKVFIAQEQMCTKRLWISNSPWTVSFRSENKRNRFIVRLSENEKAE
DYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITN
SLIASIHVADAVCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLF
PGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLER
EIRVHLAHARRKMTRAMQKHLSGKPIEHYLDASVITNGLSRAFSTGAWSH
PFRKMERVSGVVANLGRANPLQTLIDLRRTRQQVLYTGKVGDARYPHPSH
WGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFACGMEELMDD
TCTPLFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDK
DDNEVRIFTDAGRLLRPLLVVENLQKLKQEQYPFDHLLDHGILELIGIEE
EEDCNTAWGIKQLLKEPKIYTHCELDLSFLLGVSCAVVPFANHDHGRRVL
YQSQKHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVL
FNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDVQF
GKTHDSLEDDGFPFIGANMSTGDIVIGRCHSIKLKHTERGIVQKVVLSSN
DEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIV
PDIVINPHAFPSRQTPGQLLEAALSKGIACPIQAYTKLTRHATPFSTPGV
TEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDK
VKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLF
TLSDSSQMHICRKCKTYANGPYCRVCVSSDHVVRVYVPYGAKLLCQELFS
MGITLNFDTKL
3D structure
PDB8xme Transcription of the Plant RNA polymerase IV is prone to backtracking
ChainB
Resolution3.1 Å
3D
structure
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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 R245 R247 I249 F344 R420 F465 R466 K467 L498 Y499 R186 R188 I190 F285 R361 F402 R403 K404 L435 Y436
BS02 rna B K721 K921 K655 K830
BS03 dna B Y499 R1067 I1073 K1074 Y436 R970 I976 K977
Gene Ontology
Molecular Function
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
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:8xme, PDBe:8xme, PDBj:8xme
PDBsum8xme
PubMed
UniProtQ9LK40|NRPD2_ARATH DNA-directed RNA polymerases IV and V subunit 2 (Gene Name=NRPD2)

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