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Title :   SOLUTION STRUCTURE OF NELF E RRM

Authors :   K. Schweimer, J. N. Rao, L. Neumann, P. Rosch, B. M. Wohrl

Date :   10 Aug 05 (Deposition) - 16 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nelf E, Rna Recognition Motif, Alternative Splicing, Nuclear Protein, Phosphorylation, Repeat, Repressor, Rna- Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. N. Rao, L. Neumann, S. Wenzel, K. Schweimer, P. Rosch, B. M. Wohrl
Structural Studies On The Rna-Recognition Motif Of Nelf E, A Cellular Negative Transcription Elongation Factor Involved In The Regulation Of Hiv Transcription.
Biochem. J. V. 400 449 2006
PubMed-ID: 16898873 | Reference-DOI: 10.1042/BJ20060421

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.18a	ENST00000383343	18a	ENSE00001809819	HSCHR6_MHC_QBL:31917261-31917061	201	NELFE_HUMAN	-	0	0	-	-
1.18q	ENST00000383343	18q	ENSE00002158378	HSCHR6_MHC_QBL:31916623-31916541	83	NELFE_HUMAN	1-25	25	0	-	-
1.20a	ENST00000383343	20a	ENSE00001779968	HSCHR6_MHC_QBL:31915179-31915110	70	NELFE_HUMAN	26-49	24	0	-	-
1.20c	ENST00000383343	20c	ENSE00001731569	HSCHR6_MHC_QBL:31915007-31914862	146	NELFE_HUMAN	49-97	49	0	-	-
1.21ad	ENST00000383343	21ad	ENSE00001639990	HSCHR6_MHC_QBL:31913467-31913393	75	NELFE_HUMAN	98-122	25	0	-	-
1.22b	ENST00000383343	22b	ENSE00001607333	HSCHR6_MHC_QBL:31913270-31913233	38	NELFE_HUMAN	123-135	13	0	-	-
1.22f	ENST00000383343	22f	ENSE00001650692	HSCHR6_MHC_QBL:31913066-31912729	338	NELFE_HUMAN	135-248	114	0	-	-
1.23b	ENST00000383343	23b	ENSE00001661527	HSCHR6_MHC_QBL:31912616-31912472	145	NELFE_HUMAN	248-296	49	1	A:35-74	40
1.24c	ENST00000383343	24c	ENSE00001703897	HSCHR6_MHC_QBL:31912308-31912254	55	NELFE_HUMAN	296-314	19	1	A:74-92	19
1.24j	ENST00000383343	24j	ENSE00001793271	HSCHR6_MHC_QBL:31912005-31911903	103	NELFE_HUMAN	315-349	35	1	A:93-113	21
1.25d	ENST00000383343	25d	ENSE00001916146	HSCHR6_MHC_QBL:31910572-31910261	312	NELFE_HUMAN	349-380	32	0	-	-

Sequences/Alignments

NMR Structure

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:79
 aligned with NELFE_HUMAN | P18615 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:79
                                   266       276       286       296       306       316       326         
          NELFE_HUMAN   257 APRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 335
               SCOP domains d2bz2a1 A:35-113 Negative elongation factor E, NELF-E                           SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhhhhhhh.......eeee....eeeee..hhhhhhhhhhhhh.........eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RRM  PDB: A:40-110 UniProt: 262-332                                    --- PROSITE
           Transcript 1 (1) Exon 1.23b  PDB: A:35-74 [INCOMPLETE]   ------------------Exon 1.24j            Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.24c         --------------------- Transcript 1 (2)
                 2bz2 A  35 APRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 113
                                    44        54        64        74        84        94       104

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (20, 20)

NMR Structure(hide GO term definitions)

Chain A (NELFE_HUMAN | P18615)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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).
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:1900364	negative regulation of mRNA polyadenylation	Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
	GO:0034244	negative regulation of transcription elongation from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0032021	NELF complex	A complex of five proteins, designated NELF-A, -B, -C, -D, and -E in human, that can physically associate with RNP polymerase II to induce transcriptional pausing.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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