1EC6 | PR0022 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOUND TO 20-MER RNA HAIRPIN

Authors :   H. A. Lewis, K. Musunuru, K. B. Jensen, C. Edo, H. Chen

Date :   25 Jan 00 (Deposition) - 21 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)

Keywords :   Kh Domain, Alpha-Beta Fold, Rna-Binding Motif, Protein/Rna Structure, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. A. Lewis, K. Musunuru, K. B. Jensen, C. Edo, H. Chen, R. B. Darnell, S. K. Burley
Sequence-Specific Rna Binding By A Nova Kh Domain: Implications For Paraneoplastic Disease And The Fragile X Syndrome.
Cell(Cambridge, Mass. ) V. 100 323 2000
PubMed-ID: 10676814 | Reference-DOI: 10.1016/S0092-8674(00)80668-6
(for further references see the PDB file header)

Molecule 1 - 20-MER RNA HAIRPIN
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	PRODUCT OF SELEX PROTEIN BINDING STUDY
	Synthetic	:	YES

Molecule 2 - RNA-BINDING PROTEIN NOVA-2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	KH3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ASTROCYTIC NOVA-LIKE RNA-BINDING PROTEIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1EC6)

(no "Site" information available for 1EC6)

(no "SS Bond" information available for 1EC6)

(no "Cis Peptide Bond" information available for 1EC6)

(no "SAP(SNP)/Variant" information available for 1EC6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	NOVA2_HUMAN	32-99 130-196 406-473	2	- - A:5-72 B:5-72

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	NOVA2_HUMAN	32-99 130-196 406-473	1	- - A:5-72 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	NOVA2_HUMAN	32-99 130-196 406-473	1	- - - B:5-72

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000263257	1	ENSE00000858269	chr19:46476657-46476525	133	NOVA2_HUMAN	1-29	29	0	-	-
1.2	ENST00000263257	2	ENSE00001706445	chr19:46464411-46464268	144	NOVA2_HUMAN	29-77	49	0	-	-
1.3	ENST00000263257	3	ENSE00001112713	chr19:46457204-46457038	167	NOVA2_HUMAN	77-132	56	0	-	-
1.4	ENST00000263257	4	ENSE00001112712	chr19:46444203-46442771	1433	NOVA2_HUMAN	133-492	360	2	A:4-90 B:4-87	87 84

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:87
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:87
                                   414       424       434       444       454       464       474       484       
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRASNPQKV 491
               SCOP domains d1ec6a_ A: Neuro-oncological ventral antigen 2, nova-2, KH3                             SCOP domains
               CATH domains 1ec6A00 A:4-90  [code=3.30.1370.10, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: A:5-72 UniProt: 406-473                             ------------------ PROSITE
               Transcript 1 Exon 1.4  PDB: A:4-90 UniProt: 133-492 [INCOMPLETE]                                     Transcript 1
                 1ec6 A   4 MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRASNPQKV  90
                                    13        23        33        43        53        63        73        83

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:84
                                   414       424       434       444       454       464       474       484    
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRASNP 488
               SCOP domains d1ec6b_ B: Neuro-oncological ventral antigen 2, nova-2, KH3                          SCOP domains
               CATH domains 1ec6B00 B:4-87  [code=3.30.1370.10, no name defined]                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: B:5-72 UniProt: 406-473                             --------------- PROSITE
               Transcript 1 Exon 1.4  PDB: B:4-87 UniProt: 133-492 [INCOMPLETE]                                  Transcript 1
                 1ec6 B   4 MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRASNP  87
                                    13        23        33        43        53        63        73        83

Chain C from PDB  Type:RNA  Length:20
                                                    
                 1ec6 C   1 GAGGACCUAGAUCACCCCUC  20
                                    10        20

Chain D from PDB  Type:RNA  Length:20
                                                    
                 1ec6 D   1 GAGGACCUAGAUCACCCCUC  20
                                    10        20

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	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 '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein S8; Chain: A, domain 1 (139)

Homologous Superfamily: [code=3.30.1370.10, no name defined] (23)

[unclassified] (8)

1a	1ec6B00	B:4-87
1b	1ec6A00	A:4-90

(no "Pfam Domain" information available for 1EC6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NOVA2_HUMAN | Q9UNW9)

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.
biological process
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
	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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