4E3B - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TAX-INTERACTING PROTEIN-1 (TIP-1) PDZ DOMAIN BOUND TO ICAL36-L (ANSRWPTSIL) PEPTIDE

Authors :   J. F. Amacher, D. R. Madden

Date :   09 Mar 12 (Deposition) - 26 Dec 12 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Pdz-Peptide Complex, Signaling Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Amacher, P. R. Cushing, C. D. Bahl, T. Beck, D. R. Madden
Stereochemical Determinants Of C-Terminal Specificity In Pd Peptide-Binding Domains: A Novel Contribution Of The Carboxylate-Binding Loop.
J. Biol. Chem. V. 288 5114 2013
PubMed-ID: 23243314 | Reference-DOI: 10.1074/JBC.M112.401588

Molecule 1 - TAX1-BINDING PROTEIN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN (UNP RESIDUES 11-112)
	Gene	:	TAX1BP3, TIP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TIP-1, GLUTAMINASE-INTERACTING PROTEIN 3, TAX INTERACTION PROTEIN 1

Molecule 2 - ICAL50 PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	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)

(no "Ligand,Modified Residues,Ions" information available for 4E3B)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:29 , LEU A:30 , GLY A:31 , PHE A:32 , SER A:33 , ILE A:34 , GLY A:35 , GLY A:36 , GLN A:40 , ASP A:41 , GLN A:44 , ASN A:45 , THR A:59 , ARG A:60 , HIS A:91 , ARG A:95 , LEU A:98 , HOH A:215 , HOH A:224 , HOH A:296 , HOH C:101 , HOH C:102 , HOH C:103 , HOH C:104 , HOH C:107 , HOH C:108 , HOH C:109 , HOH C:110 , HOH C:111 , HOH C:112 , HOH C:113 , HOH C:114	BINDING SITE FOR CHAIN C OF ICAL50 PEPTIDE
2	AC2	SOFTWARE	ILE B:29 , LEU B:30 , GLY B:31 , PHE B:32 , SER B:33 , ILE B:34 , GLY B:35 , GLY B:36 , GLN B:40 , ASP B:41 , GLN B:44 , ASN B:45 , ASP B:50 , THR B:59 , ARG B:60 , HIS B:91 , ARG B:95 , LEU B:98 , HOH B:215 , HOH B:273 , HOH D:101 , HOH D:102 , HOH D:103 , HOH D:104 , HOH D:105 , HOH D:106 , HOH D:107 , HOH D:108 , HOH D:110 , HOH D:111 , HOH D:112 , HOH D:113 , HOH D:116 , HOH D:117 , HOH D:118 , HOH D:119	BINDING SITE FOR CHAIN D OF ICAL50 PEPTIDE

(no "SS Bond" information available for 4E3B)

(no "Cis Peptide Bond" information available for 4E3B)

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	34	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	34	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	34	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:16-113 B:16-113

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:16-113 -

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:16-113

(no "Exon" information available for 4E3B)

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:102
 aligned with TX1B3_HUMAN | O14907 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:102
                                    20        30        40        50        60        70        80        90       100       110  
          TX1B3_HUMAN    11 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQ 112
               SCOP domains d4e3ba_ A: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------T------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:16-113 UniProt: 15-112                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4e3b A  12 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQ 113
                                    21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with TX1B3_HUMAN | O14907 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:102
                                    20        30        40        50        60        70        80        90       100       110  
          TX1B3_HUMAN    11 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQ 112
               SCOP domains d4e3bb_ B: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------T------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:16-113 UniProt: 15-112                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4e3b B  12 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQ 113
                                    21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....eeee Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4e3b C   3 SRWPTSIL  10

Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .....eeee Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4e3b D   2 NSRWPTSIL  10

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d4e3ba_	A:
1b	d4e3bb_	B:

(no "CATH Domain" information available for 4E3B)

(no "Pfam Domain" information available for 4E3B)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4e3b)

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4e3b)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4e3b
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TX1B3_HUMAN \| O14907
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TX1B3_HUMAN \| O14907
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TX1B3_HUMAN \| O14907	:	2kg2 2l4s 2l4t 2vz5 3gj9 3sfj 4nnl 4nnm

3sfj	TIP-1 PDZ DOMAIN BOUND TO ICAL36 (ANSRWPTSII) PEPTIDE
4e34
4e35

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File