3CLJ - JenaLib

Title :   STRUCTURE OF THE RNA POLYMERASE II CTD-INTERACTING DOMAIN OF NRD1

Authors :   L. Vasiljeva, M. Kim, H. Mutschler, S. Buratowski, A. Meinhart

Date :   19 Mar 08 (Deposition) - 29 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Ctd-Interacting Domain, Nucleus, Phosphoprotein, Rna Polymerase Ii Binding Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Vasiljeva, M. Kim, H. Mutschler, S. Buratowski, A. Meinhart
The Nrd1-Nab3-Sen1 Termination Complex Interacts With The Ser5-Phosphorylated Rna Polymerase Ii C-Terminal Domain.
Nat. Struct. Mol. Biol. V. 15 795 2008
PubMed-ID: 18660819 | Reference-DOI: 10.1038/NSMB.1468

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:146
 aligned with NRD1_YEAST | P53617 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           NRD1_YEAST     1 MQQDDDFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSKCFAMDI 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CID  PDB: A:5-151 UniProt: 1-153                                                                                                                         - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clj A   5 M----DFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSN----SNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSKCFAAAL 154
                            |    |  10        20        30        40        50        60        70        80  |    |90       100       110       120       130       140       150    
                            |    6                                                                           83   88                                                                  
                            5

Legend:		→ Mismatch	(orange background)
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		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NRD1_YEAST | P53617)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0001068	transcription regulatory region RNA binding	Interacting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon.
biological process
	GO:0071034	CUT catabolic process	The chemical reactions and pathways resulting in the breakdown of cryptic unstable transcripts (CUTs).
	GO:0071041	antisense RNA transcript catabolic process	The chemical reactions and pathways resulting in the breakdown of antisense transcripts, i.e. transcripts that were produced from the antisense strand of a gene that produces a gene product and which often have a regulatory effect on the transcription of that gene product.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0071028	nuclear mRNA surveillance	The set of processes involved in identifying and degrading defective or aberrant mRNAs within the nucleus.
	GO:0034472	snRNA 3'-end processing	Any process involved in forming the mature 3' end of an snRNA molecule.
	GO:0031126	snoRNA 3'-end processing	Any process involved in forming the mature 3' end of a snoRNA molecule.
	GO:0042780	tRNA 3'-end processing	The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.
	GO:0030847	termination of RNA polymerase II transcription, exosome-dependent	The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
cellular component
	GO:0035649	Nrd1 complex	A complex that functions in transcription termination of RNA polymerase II transcribed non-coding RNAs. This complex interacts with the carboxy-terminal domain (CTD) of PolII and the terminator sequences in the nascent RNA transcript. In yeast this complex consists of Nrd1p, Nab3p, and Sen1p.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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