3R68 - JenaLib

Title :   MOLECULAR ANALYSIS OF THE PDZ3 DOMAIN OF PDZK1

Authors :   O. Kocher, G. Birrane, M. Krieger

Date :   21 Mar 11 (Deposition) - 18 May 11 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Pdz Domain, Adaptor Protein, Sr-Bi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Kocher, G. Birrane, A. Yesilaltay, S. Shechter, R. Pal, K. Daniels, M. Krieger
Identification Of The Pdz3 Domain Of The Adaptor Protein Pdzk1 As A Second, Physiologically Functional Binding Site For The C Terminus Of The High Density Lipoprotein Receptor Scavenger Receptor Class B Type I.
J. Biol. Chem. V. 286 25171 2011
PubMed-ID: 21602281 | Reference-DOI: 10.1074/JBC.M111.242362

Compounds

Molecule 1 - NA(+)/H(+) EXCHANGE REGULATORY COFACTOR NHE-RF3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-3
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ3 (UNP RESIDUES 237-323)
	Gene	:	CAP70, NHERF3, PDZK1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	NHERF-3, CFTR-ASSOCIATED PROTEIN OF 70 KDA, NA(+)/H(+) EXCHANGER REGULATORY FACTOR 3, NA/PI COTRANSPORTER C-TERMINAL- ASSOCIATED PROTEIN 1, NAPI-CAP1, PDZ DOMAIN-CONTAINING PROTEIN 1, SODIUM-HYDROGEN EXCHANGER REGULATORY FACTOR 3

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	CL	5	Ligand/Ion	CHLORIDE ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:117 , HOH A:137 , LYS A:269 , ASP A:270	BINDING SITE FOR RESIDUE ACT A 1
02	AC2	SOFTWARE	ZN A:4 , HOH A:24 , HOH A:69 , HIS A:239 , PRO A:241 , ARG A:242 , LYS A:283 , VAL A:289 , GLU A:297 , ASP A:321	BINDING SITE FOR RESIDUE ACT A 2
03	AC3	SOFTWARE	CL A:9 , HOH A:92 , HOH A:108 , ASN A:251 , GLY A:252 , TYR A:253 , GLY A:254 , PHE A:255 , TYR A:256	BINDING SITE FOR RESIDUE EDO A 3
04	AC4	SOFTWARE	ACT A:2 , HIS A:239 , GLU A:297 , ASP A:321	BINDING SITE FOR RESIDUE ZN A 4
05	AC5	SOFTWARE	ZN A:6 , CL A:8 , CL A:9 , HOH A:108 , ASP A:302	BINDING SITE FOR RESIDUE ZN A 5
06	AC6	SOFTWARE	ZN A:5 , ZN A:7 , HOH A:29 , HOH A:34 , HOH A:40 , HOH A:108	BINDING SITE FOR RESIDUE ZN A 6
07	AC7	SOFTWARE	ZN A:6 , CL A:10 , HOH A:40 , HOH A:109 , HIS A:301	BINDING SITE FOR RESIDUE ZN A 7
08	AC8	SOFTWARE	ZN A:5 , LYS A:248 , ASP A:302 , ARG A:309	BINDING SITE FOR RESIDUE CL A 8
09	AC9	SOFTWARE	EDO A:3 , ZN A:5 , GLY A:252 , TYR A:253 , ASP A:302	BINDING SITE FOR RESIDUE CL A 9
10	BC1	SOFTWARE	ZN A:7 , LEU A:257 , ARG A:258 , HIS A:301	BINDING SITE FOR RESIDUE CL A 10
11	BC2	SOFTWARE	CL A:13 , CA A:14 , GLU A:306	BINDING SITE FOR RESIDUE CL A 11
12	BC3	SOFTWARE	CA A:14 , ARG A:309	BINDING SITE FOR RESIDUE CA A 12
13	BC4	SOFTWARE	CL A:11 , CA A:14 , GLU A:306	BINDING SITE FOR RESIDUE CL A 13
14	BC5	SOFTWARE	CL A:11 , CA A:12 , CL A:13 , GLU A:306	BINDING SITE FOR RESIDUE CA A 14

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_MOUSE	9-90 135-215 243-323 378-454	1	- - A:243-323 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_MOUSE	9-90 135-215 243-323 378-454	1	- - A:243-323 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_MOUSE	9-90 135-215 243-323 378-454	2	- - A:243-323 -

Exons (0, 0)

Sequences/Alignments

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:85
 aligned with NHRF3_MOUSE | Q9JIL4 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:87
                                   246       256       266       276       286       296       306       316       
          NHRF3_MOUSE   237 LPHQPRVVVIKKGSNGYGFYLRAGPEQKGQIIKDIEPGSPAEAAGLKNNDLVVAVNGKSVEALDHDGVVEMIRKGGDQTTLLVLDKE 323
               SCOP domains d3r68a_ A: automated mat  ches                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----PDZ-3r68A01 A:242-3  20                                                        --- Pfam domains
         Sec.struct. author .....eeeeee........eeee.--...eeee.....hhhhhhh....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: A:243-323 UniProt: 243-323                                              PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3r68 A 237 SPHQPRVVVIKKGSNGYGFYLRAG--QKGQIIKDIEPGSPAEAAGLKNNDLVVAVNGKSVEALDHDGVVEMIRKGGDQTTLLVLDKE 323
                                   246       256   |  |266       276       286       296       306       316       
                                                 260  |                                                            
                                                    263

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

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (NHRF3_MOUSE | Q9JIL4)

molecular function
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	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:0015879	carnitine transport	The directed movement of carnitine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
	GO:0090002	establishment of protein localization to plasma membrane	The directed movement of a protein to a specific location in the plasma membrane.
	GO:0034767	positive regulation of ion transmembrane transport	Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0090314	positive regulation of protein targeting to membrane	Any process that increases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0044070	regulation of anion transport	Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0031526	brush border membrane	The portion of the plasma membrane surrounding the brush border.
	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: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.

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Description