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Description

Title :   SOLUTION STRUCTURE OF THE THIRD PDZ DOMAIN OF HUMAN INAD-LIKE PROTEIN

Authors :   K. Inoue, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   24 Apr 06 (Deposition) - 24 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Pdz Domain, Inad-Like Protein, Inadl Protein, Hinadl, Pals1- Associated Tight Junction Protein, Protein Associated To Tight Junctions, Inadl, Patj, 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 :   K. Inoue, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Third Pdz Domain Of Human Inad-Like Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - INAD-LIKE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050627-17
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN
	Gene	:	INADL, PATJ
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	INADL PROTEIN, HINADL, PALS1-ASSOCIATED TIGHT JUNCTION PROTEIN, PROTEIN ASSOCIATED TO TIGHT JUNCTIONS

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 2DMZ)

Sites (0, 0)

(no "Site" information available for 2DMZ)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_027989	E	362	A	INADL_HUMAN	Polymorphism	1286823	A	E	15	A
2	UniProt	VAR_027990	I	400	V	INADL_HUMAN	Polymorphism	7516332	A	V	53	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	INADL_HUMAN	134-221 248-328 365-453 553-639 686-758 1068-1160 1239-1322 1437-1520 1533-1615 1676-1762	1	- - A:18-106 - - - - - - -

Exons (5, 5)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000371158	1	ENSE00001341045	chr1:62208149-62208227	79	INADL_HUMAN	-	0	0	-	-
1.2	ENST00000371158	2	ENSE00002140234	chr1:62228530-62228586	57	INADL_HUMAN	1-8	8	0	-	-
1.3	ENST00000371158	3	ENSE00001653283	chr1:62228685-62228851	167	INADL_HUMAN	8-63	56	0	-	-
1.4	ENST00000371158	4	ENSE00001596231	chr1:62231951-62232145	195	INADL_HUMAN	64-128	65	0	-	-
1.5	ENST00000371158	5	ENSE00001747515	chr1:62234955-62235094	140	INADL_HUMAN	129-175	47	0	-	-
1.6	ENST00000371158	6	ENSE00001756534	chr1:62237103-62237298	196	INADL_HUMAN	175-240	66	0	-	-
1.7	ENST00000371158	7	ENSE00001714688	chr1:62240878-62241006	129	INADL_HUMAN	241-283	43	0	-	-
1.8	ENST00000371158	8	ENSE00001680186	chr1:62253426-62253644	219	INADL_HUMAN	284-356	73	1	A:1-9 (gaps)	40
1.9	ENST00000371158	9	ENSE00001684863	chr1:62257020-62257119	100	INADL_HUMAN	357-390	34	1	A:10-43	34
1.10	ENST00000371158	10	ENSE00001621384	chr1:62261139-62261230	92	INADL_HUMAN	390-420	31	1	A:43-73	31
1.11	ENST00000371158	11	ENSE00001704241	chr1:62262959-62263100	142	INADL_HUMAN	421-468	48	1	A:74-121	48
1.12	ENST00000371158	12	ENSE00001701190	chr1:62267295-62267441	147	INADL_HUMAN	468-517	50	1	A:121-129 (gaps)	16
1.13a	ENST00000371158	13a	ENSE00001634823	chr1:62271120-62271196	77	INADL_HUMAN	517-542	26	0	-	-
1.14	ENST00000371158	14	ENSE00001180884	chr1:62274146-62274202	57	INADL_HUMAN	543-561	19	0	-	-
1.15	ENST00000371158	15	ENSE00001313645	chr1:62288617-62288751	135	INADL_HUMAN	562-606	45	0	-	-
1.16	ENST00000371158	16	ENSE00001011133	chr1:62293094-62293255	162	INADL_HUMAN	607-660	54	0	-	-
1.17	ENST00000371158	17	ENSE00001011140	chr1:62299326-62299457	132	INADL_HUMAN	661-704	44	0	-	-
1.18	ENST00000371158	18	ENSE00001011138	chr1:62321702-62321911	210	INADL_HUMAN	705-774	70	0	-	-
1.19	ENST00000371158	19	ENSE00001011136	chr1:62327223-62327339	117	INADL_HUMAN	775-813	39	0	-	-
1.20a	ENST00000371158	20a	ENSE00001011158	chr1:62329910-62330305	396	INADL_HUMAN	814-945	132	0	-	-
1.22a	ENST00000371158	22a	ENSE00001011157	chr1:62340915-62341038	124	INADL_HUMAN	946-987	42	0	-	-
1.23	ENST00000371158	23	ENSE00001011142	chr1:62349909-62350080	172	INADL_HUMAN	987-1044	58	0	-	-
1.24	ENST00000371158	24	ENSE00001011134	chr1:62365255-62365326	72	INADL_HUMAN	1044-1068	25	0	-	-
1.25	ENST00000371158	25	ENSE00001011132	chr1:62366954-62367131	178	INADL_HUMAN	1068-1127	60	0	-	-
1.26	ENST00000371158	26	ENSE00001011151	chr1:62374044-62374154	111	INADL_HUMAN	1128-1164	37	0	-	-
1.27	ENST00000371158	27	ENSE00001011139	chr1:62380259-62380336	78	INADL_HUMAN	1165-1190	26	0	-	-
1.28b	ENST00000371158	28b	ENSE00001011147	chr1:62393402-62393501	100	INADL_HUMAN	1191-1224	34	0	-	-
1.30a	ENST00000371158	30a	ENSE00001170290	chr1:62455840-62456036	197	INADL_HUMAN	1224-1289	66	0	-	-
1.32	ENST00000371158	32	ENSE00001011145	chr1:62483528-62483619	92	INADL_HUMAN	1290-1320	31	0	-	-
1.33	ENST00000371158	33	ENSE00001011135	chr1:62503649-62503721	73	INADL_HUMAN	1320-1344	25	0	-	-
1.34	ENST00000371158	34	ENSE00001066757	chr1:62516638-62516730	93	INADL_HUMAN	1345-1375	31	0	-	-
1.35a	ENST00000371158	35a	ENSE00001066756	chr1:62545122-62545239	118	INADL_HUMAN	1376-1415	40	0	-	-
1.36	ENST00000371158	36	ENSE00001066761	chr1:62550187-62550320	134	INADL_HUMAN	1415-1459	45	0	-	-
1.38	ENST00000371158	38	ENSE00001066759	chr1:62574109-62574192	84	INADL_HUMAN	1460-1487	28	0	-	-
1.39a	ENST00000371158	39a	ENSE00002161466	chr1:62579725-62579918	194	INADL_HUMAN	1488-1552	65	0	-	-
1.40	ENST00000371158	40	ENSE00001775347	chr1:62582204-62582351	148	INADL_HUMAN	1552-1601	50	0	-	-
1.41a	ENST00000371158	41a	ENSE00001639463	chr1:62582804-62582890	87	INADL_HUMAN	1602-1630	29	0	-	-
1.42b	ENST00000371158	42b	ENSE00001668046	chr1:62586853-62586967	115	INADL_HUMAN	1631-1669	39	0	-	-
1.43	ENST00000371158	43	ENSE00001794870	chr1:62588693-62588730	38	INADL_HUMAN	1669-1681	13	0	-	-
1.44a	ENST00000371158	44a	ENSE00001618976	chr1:62593644-62593766	123	INADL_HUMAN	1682-1722	41	0	-	-
1.45	ENST00000371158	45	ENSE00001716409	chr1:62594513-62594617	105	INADL_HUMAN	1723-1757	35	0	-	-
1.46	ENST00000371158	46	ENSE00001721876	chr1:62613956-62614062	107	INADL_HUMAN	1758-1793	36	0	-	-
1.48b	ENST00000371158	48b	ENSE00001714413	chr1:62626580-62629592	3013	INADL_HUMAN	1793-1801	9	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:129
 aligned with INADL_HUMAN | Q8NI35 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:167
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       
          INADL_HUMAN   317 GNSVRMLVARDPAGDISVTPPAPAALPVALPTVASKGPGSDSSLFETYNVELVRKDGQSLGIRIVGYVGTSHTGEASGIYVKSIIPGSAAYHNGHIQVNDKIVAVDGVNIQGFANHDVVEVLRNAGQVVHLTLVRRKTSSSTSPLEPPSDRGTVVEPLKPPALFLTG 483
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------2dmzA01 A:13-106  [code=2.30.42.10, no name defined]                                          ------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------------------------------....-......eeeeeeee.........eeeeee..........eeeeeee...hhhhhhh.......eeee........hhhhhhhhhhhh...eeeeeeee......................-------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------A-------------------------------------V----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PDZ  PDB: - ------------------------------------PDZ  PDB: A:18-106 UniProt: 365-453                                                      ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:1-9 (gaps) [INCOMPLETE]---------------------------------Exon 1.10  PDB: A:43-73        Exon 1.11  PDB: A:74-121 UniProt: 421-468       --------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.9  PDB: A:10-43            -----------------------------------------------------------------------------Exon 1.12        Transcript 1 (2)
                 2dmz A   1 GSS------------------------------GSSG-GSDSSLFETYNVELVRKDGQSLGIRIVGYVGTSHTGEASGIYVKSVIPGSAAYHNGHIQVNDKIVAVDGVNIQGFANHDVVEVLRNAGQVVHLTLVRRKTSSSTSPLEPPSDRGTVSGPS-------SG 129
                              |      -         -         -   |  | |9        19        29        39        49        59        69        79        89        99       109       119       | -     | 
                              3                              4  7 8                                                                                                                    127     128

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 (0, 0)

(no "SCOP Domain" information available for 2DMZ)

CATH Domains (1, 1)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

Homologous Superfamily: [code=2.30.42.10, no name defined] (191)

Human (Homo sapiens) (120)

2dmzA01

A:13-106

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2DMZ)

Gene Ontology (13, 13)

NMR Structure(hide GO term definitions)

Chain A (INADL_HUMAN | Q8NI35)

molecular function
	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:0070830	bicellular tight junction assembly	The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
cellular component
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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Related Entries

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UniProtKB/Swiss-Prot
	INADL_HUMAN \| Q8NI35	:	1vf6 2d92 2daz 2db5 2dlu 2dm8 2ehr 4q2n

Related Entries Specified in the PDB File

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