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Title :   CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN

Authors :   H. A. Lewis, H. Chen, C. Edo, R. J. Buckanovich, Y. Y. L. Yang, K. Musunuru, R. Zhong, R. B. Darnell, S. K. Burley

Date :   12 Jan 00 (Deposition) - 18 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Kh Domain, Alpha-Beta Fold Rna-Binding Motif, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. A. Lewis, H. Chen, C. Edo, R. J. Buckanovich, Y. Y. Yang, K. Musunuru, R. Zhong, R. B. Darnell, S. K. Burley
Crystal Structures Of Nova-1 And Nova-2 K-Homology Rna-Binding Domains.
Structure Fold. Des. V. 7 191 1999
PubMed-ID: 10368286 | Reference-DOI: 10.1016/S0969-2126(99)80025-2
(for further references see the PDB file header)

Molecule 1 - RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
	Cell	:	NEURON
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Fragment	:	THIRD KH DOMAIN OF NOVA-2
	Mutation	:	YES
	Organ	:	BRAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1DTJ)

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

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

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

Asymmetric Unit (1, 4)

	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	4	- - A:5-72 B:5-72 C:5-72 D: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 - -

Biological Unit 3 (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	- - - - C:5-72 -

Biological Unit 4 (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	- - - - - D:5-72

Asymmetric Unit (1, 4)

	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	4	A:4-77 B:4-79 (gaps) C:4-77 (gaps) D:4-76 (gaps)	74 76 74 73

Asymmetric 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:74
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:74
                                   414       424       434       444       454       464       474    
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT 478
               SCOP domains d1dtja_ A: Neuro-oncological ventral antigen 2, nova-2, KH3                SCOP domains
               CATH domains 1dtjA00 A:4-77  [code=3.30.1370.10, no name defined]                       CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhh..hhhhhhhhhhhh................eeeeeeeehhhhhhhhhhhhhhhh. 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:4-77 UniProt: 133-492 [INCOMPLETE]                        Transcript 1
                 1dtj A   4 MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT  77
                                    13        23        33        43        53        63        73

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:76
                                   414       424       434       444       454       464       474      
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE 480
               SCOP domains d1dtjb_ B: Neuro-      oncological vent        ral antigen 2, nova-2, KH3    SCOP domains
               CATH domains 1dtjB00 B:4-79  [      code=3.30.1370.1        0, no name defined]           CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhh------hhhhhhhhhh......--------..eeeeeeeehhhhhhhhhhhhhhh.... 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:4-79 (gaps) UniProt: 133-492 [INCOMPLETE]                   Transcript 1
                 1dtj B   4 MKELVEMAVPENLVGAI------TLVEYQELTGARIQIS--------TRNRRVTITGSPAATQAAQYLISQRVTYE  79
                                    13      |  -   |    33        |-       |53        63        73      
                                           20     27             42       51

Chain C from PDB  Type:PROTEIN  Length:66
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:74
                                   414       424       434       444       454       464       474    
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT 478
               SCOP domains d1dtjc_ C: Neuro-oncological ventral an        tigen 2, nova-2, KH3        SCOP domains
               CATH domains 1dtjC00 C:4-77  [code=3.30.1370.10, no         name defined]               CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhh..hhhhhhhhhhhh.eeee.--------..eeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: C:5-72 UniProt: 406-473                             ----- PROSITE
               Transcript 1 Exon 1.4  PDB: C:4-77 (gaps) UniProt: 133-492 [INCOMPLETE]                 Transcript 1
                 1dtj C   4 MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQIS--------TRNRRVTITGSPAATQAAQYLISQRVT  77
                                    13        23        33        |-       |53        63        73    
                                                                 42       51

Chain D from PDB  Type:PROTEIN  Length:64
 aligned with NOVA2_HUMAN | Q9UNW9 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:73
                                   414       424       434       444       454       464       474   
          NOVA2_HUMAN   405 AKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV 477
               SCOP domains d1dtjd_ D: Neuro-oncological ventral an         tigen 2, nova-2, KH3      SCOP domains
               CATH domains 1dtjD00 D:4-76  [code=3.30.1370.10, no          name defined]             CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eeee.---------.eeeeeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: D:5-72 UniProt: 406-473                             ---- PROSITE
               Transcript 1 Exon 1.4  PDB: D:4-76 (gaps) UniProt: 133-492 [INCOMPLETE]                Transcript 1
                 1dtj D   4 MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQIS---------RNRRVTITGSPAATQAAQYLISQRV  76
                                    13        23        33        |-        53        63        73   
                                                                 42        52

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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)

Human (Homo sapiens) (13)

1a	1dtjA00	A:4-77
1b	1dtjC00	C:4-77
1c	1dtjD00	D:4-76
1d	1dtjB00	B:4-79

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	NOVA2_HUMAN \| Q9UNW9	:	1ec6

1dt4	CRYSTAL STRUCTURE OF NOVA-1 KH3 K-HOMOLOGY RNA-BINDING DOMAIN
1ec6	SAME PROTEIN WITH RNA

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