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Description

Title :   SOLUTION STRUCTURE OF THE WW DOMAIN FROM THE HUMAN AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 3, APBB3

Authors :   S. Ohnishi, M. Yoneyama, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   03 Apr 07 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Fe65-Like Protein 2, Ww Domain, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ohnishi, M. Yoneyama, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama
Solution Structure Of The Ww Domain From The Human Amyloid Beta A4 Precursor Protein-Binding Family B Member 3, Apbb3
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 3
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P061016-08
	Expression System Vector Type	:	PLASMID
	Fragment	:	WW DOMAIN
	Gene	:	APBB3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	FE65-LIKE PROTEIN 2, FE65L2

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YSC)

Sites (0, 0)

(no "Site" information available for 2YSC)

SS Bonds (0, 0)

(no "SS Bond" information available for 2YSC)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2YSC)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2YSC)

PROSITE Motifs (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WW_DOMAIN_2	PS50020	WW/rsp5/WWP domain profile.	APBB3_HUMAN	29-61	1	A:8-39
2	WW_DOMAIN_1	PS01159	WW/rsp5/WWP domain signature.	APBB3_HUMAN	35-59	1	A:13-37

Exons (1, 1)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.13b	ENST00000357560	13b	ENSE00001812697	chr5:139944274-139943782	493	APBB3_HUMAN	1-17	17	0	-	-
1.13q	ENST00000357560	13q	ENSE00000765161	chr5:139943500-139943337	164	APBB3_HUMAN	17-71	55	1	A:1-39 (gaps)	41
1.13t	ENST00000357560	13t	ENSE00000765158	chr5:139943255-139943179	77	APBB3_HUMAN	72-97	26	0	-	-
1.14c	ENST00000357560	14c	ENSE00000765156	chr5:139942308-139942248	61	APBB3_HUMAN	97-117	21	0	-	-
1.14h	ENST00000357560	14h	ENSE00000765154	chr5:139942084-139941938	147	APBB3_HUMAN	118-166	49	0	-	-
1.15c	ENST00000357560	15c	ENSE00001162509	chr5:139941812-139941685	128	APBB3_HUMAN	167-209	43	0	-	-
1.15n	ENST00000357560	15n	ENSE00001727736	chr5:139941434-139941429	6	APBB3_HUMAN	209-211	3	0	-	-
1.15s	ENST00000357560	15s	ENSE00001162483	chr5:139941286-139941172	115	APBB3_HUMAN	211-249	39	0	-	-
1.16	ENST00000357560	16	ENSE00000765148	chr5:139941034-139940950	85	APBB3_HUMAN	250-278	29	0	-	-
1.17a	ENST00000357560	17a	ENSE00000765146	chr5:139940686-139940603	84	APBB3_HUMAN	278-306	29	0	-	-
1.18c	ENST00000357560	18c	ENSE00001162463	chr5:139940339-139940224	116	APBB3_HUMAN	306-344	39	0	-	-
1.19b	ENST00000357560	19b	ENSE00001771362	chr5:139940089-139939898	192	APBB3_HUMAN	345-408	64	0	-	-
1.20c	ENST00000357560	20c	ENSE00001837726	chr5:139938406-139937857	550	APBB3_HUMAN	409-486	78	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
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Chain A from PDB  Type:PROTEIN  Length:39
 aligned with APBB3_HUMAN | O95704 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:41
                                    30        40        50        60 
           APBB3_HUMAN   21 GDHSLEVEAGLPPGWRKIHDAAGTYYWHVPSGSTQWQRPTW 61
               SCOP domains ---------d2ysca1 A:8-33            ------ SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------WW-2yscA01 A:9-37            -- Pfam domains
         Sec.struct. author .--...........eeeeee..eeeeee.....ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                PROSITE (1) --------WW_DOMAIN_2  PDB: A:8-39          PROSITE (1)
                PROSITE (2) --------------WW_DOMAIN_1  PDB: A:13-37-- PROSITE (2)
               Transcript 1 Exon 1.13q  PDB: A:1-39 (gaps)            Transcript 1
                  2ysc A  1 G--SSGSSGGLPPGWRKIHDAAGTYYWHVPSGSTQWQRPTW 39
                            |  |     8        18        28        38 
                            |  2                                     
                            1

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)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: WW domain-like (101)

Superfamily: WW domain (80)

Family: WW domain (69)

Protein domain: Amyloid beta A4 precursor protein-binding family B member 3, APBB3 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2ysca1

A:8-33

CATH Domains (0, 0)

(no "CATH Domain" information available for 2YSC)

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: WW] (77)

Family: WW (77)

Homo sapiens (Human) (62)

WW-2yscA01

A:9-37

Gene Ontology (7, 7)

NMR Structure(hide GO term definitions)

Chain A (APBB3_HUMAN | O95704)

molecular function
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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Related Entries

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	APBB3_HUMAN \| O95704	:	2dyq

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