3GJ9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF TIP-1 IN COMPLEX WITH C-TERMINAL OF KIR2.3

Authors :   Y. Shen

Date :   08 Mar 09 (Deposition) - 15 Dec 09 (Release) - 15 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Tip-1, Kir2. 3, Pdz Domain, Cytoplasm, Nucleus, Phosphoprotein, Wnt Signaling Pathway, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Yan, H. Zhou, J. Zhang, C. Shi, X. Xie, Y. Wu, C. Tian, Y. Shen, J. Long
Molecular Mechanism Of Inward Rectifier Potassium Channel 2. 3 Regulation By Tax-Interacting Protein-1
J. Mol. Biol. V. 392 967 2009
PubMed-ID: 19635485 | Reference-DOI: 10.1016/J.JMB.2009.07.060
(for further references see the PDB file header)

Molecule 1 - TAX1-BINDING PROTEIN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TAX INTERACTION PROTEIN 1, TIP-1, GLUTAMINASE- INTERACTING PROTEIN 3

Molecule 2 - C-TERMINAL PEPTIDE FROM INWARD RECTIFIER POTASSIUM CHANNEL 4
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS
	Synonym	:	C-TERMINAL PEPTIDE OF INWARD RECTIFIER K(+) CHANNEL KIR2.3
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:19 , GLU A:103 , GLU B:103 , ZN B:125	BINDING SITE FOR RESIDUE ZN A 125
2	AC2	SOFTWARE	GLU A:103 , ZN A:125 , HIS B:19 , GLU B:103	BINDING SITE FOR RESIDUE ZN B 125
3	AC3	SOFTWARE	GLU A:17 , GLU B:62 , GLU B:67 , HOH B:135 , HOH B:164	BINDING SITE FOR RESIDUE ZN B 126
4	AC4	SOFTWARE	GLU A:62 , GLU A:67 , HOH A:128 , GLU B:17 , HOH B:134	BINDING SITE FOR RESIDUE ZN B 127
5	AC5	SOFTWARE	ARG A:15 , GLN A:79 , GLY A:82 , ARG A:106	BINDING SITE FOR RESIDUE CL A 126
6	AC6	SOFTWARE	GLN A:72 , ILE A:73 , ARG B:106	BINDING SITE FOR RESIDUE CL A 127
7	AC7	SOFTWARE	ARG B:15 , GLN B:79 , GLY B:82 , ARG B:106	BINDING SITE FOR RESIDUE CL B 128
8	AC8	SOFTWARE	ARG A:106 , ILE B:73	BINDING SITE FOR RESIDUE CL B 129

(no "SS Bond" information available for 3GJ9)

(no "Cis Peptide Bond" information available for 3GJ9)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073966	I	33	T	TX1B3_HUMAN	Unclassified	---	A/B	I	33	T

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073966	I	33	T	TX1B3_HUMAN	Unclassified	---	A	I	33	T

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073966	I	33	T	TX1B3_HUMAN	Unclassified	---	B	I	33	T

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	TX1B3_HUMAN	15-112	2	A:15-112 B:15-112

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	TX1B3_HUMAN	15-112	1	A:15-112 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	TX1B3_HUMAN	15-112	1	- B:15-112

(no "Exon" information available for 3GJ9)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:108
 aligned with TX1B3_HUMAN | O14907 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:108
                                    19        29        39        49        59        69        79        89        99       109        
          TX1B3_HUMAN    10 TAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKA 117
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3gj9A00 A:10-117  [code=2.30.42.10, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -----------------------T------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:15-112 UniProt: 15-112                                                                ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3gj9 A  10 TAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKA 117
                                    19        29        39        49        59        69        79        89        99       109

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with TX1B3_HUMAN | O14907 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:106
                                    20        30        40        50        60        70        80        90       100       110      
          TX1B3_HUMAN    11 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQK 116
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gj9B00 B:11-116  [code=2.30.42.10, no name defined]                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.eee..eee..eeeee...................eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------T----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:15-112 UniProt: 15-112                                                                ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3gj9 B  11 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQK 116
                                    20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:6
 aligned with KCNJ4_HUMAN | P48050 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:6
          KCNJ4_HUMAN   440 RRESAI 445
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3gj9 C 440 RRESAI 445

Chain D from PDB  Type:PROTEIN  Length:6
 aligned with KCNJ4_HUMAN | P48050 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:6
          KCNJ4_HUMAN   440 RRESAI 445
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3gj9 D 440 RRESAI 445

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 '\|'

(no "SCOP Domain" information available for 3GJ9)

Asymmetric Unit

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)

1a	3gj9B00	B:11-116
1b	3gj9A00	A:10-117

(no "Pfam Domain" information available for 3GJ9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TX1B3_HUMAN | O14907)

molecular function
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	GO:0030178	negative regulation of Wnt signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:2000009	negative regulation of protein localization to cell surface	Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to the cell surface.
	GO:0030111	regulation of Wnt signaling pathway	Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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.
	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.

Chain C,D (KCNJ4_HUMAN | P48050)

molecular function
	GO:0015467	G-protein activated inward rectifier potassium channel activity	Enables the transmembrane transfer of a potassium ion by an inwardly-rectifying voltage-gated channel, where the inward rectification is due to a voltage-dependent block of the channel pore by a G protein. An inwardly rectifying current-voltage relation is one where at any given driving force the inward flow of K+ ions exceeds the outward flow for the opposite driving force.
	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:0005242	inward rectifier potassium channel activity	Enables the transmembrane transfer of a potassium ion by an inwardly-rectifying voltage-gated channel. An inwardly rectifying current-voltage relation is one where at any given driving force the inward flow of K+ ions exceeds the outward flow for the opposite driving force. The inward-rectification is due to a voltage-dependent block of the channel pore by a specific ligand or ligands, and as a result the macroscopic conductance depends on the difference between membrane voltage and the K+ equilibrium potential rather than on membrane voltage itself.
	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:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0061337	cardiac conduction	Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0010107	potassium ion import	The directed movement of potassium ions into a cell or organelle.
	GO:0006813	potassium ion transport	The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	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:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	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:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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	TX1B3_HUMAN \| O14907	:	2kg2 2l4s 2l4t 2vz5 3sfj 4e3b 4nnl 4nnm

3diw	TIP-1 IN COMPLEX WITH C-TERMINAL B-CATENIN
3dj1	TIP-1 WILD TYPE
3dj3	C-TERMINAL TRUNCATION OF TIP-1

Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

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