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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AXIN DIX DOMAIN

Authors :   N. Shibata, T. Hanamura, R. Yamamoto, Y. Ueda, H. Yamamoto, A. Kikuchi, Y. Higuchi

Date :   08 Nov 04 (Deposition) - 14 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Shibata, T. Hanamura, R. Yamamoto, Y. Ueda, H. Yamamoto, A. Kikuchi, Y. Higuchi
Crystal Structure Of Axin Dix Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - AXIN 1 PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALC2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DIX DOMAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AXIS INHIBITION PROTEIN 1, RAXIN

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	BEZ	1	Ligand/Ion	BENZOIC ACID
2	HG	9	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:184 , CYS A:750 , SER A:752	BINDING SITE FOR RESIDUE HG A 1094
2	AC2	SOFTWARE	BEZ A:501 , PHE A:759 , CYS A:760	BINDING SITE FOR RESIDUE HG A 1095
3	AC3	SOFTWARE	CYS A:803	BINDING SITE FOR RESIDUE HG A 1096
4	AC4	SOFTWARE	CYS B:750 , SER B:752	BINDING SITE FOR RESIDUE HG B 1194
5	AC5	SOFTWARE	PHE B:759 , CYS B:760 , TYR B:790	BINDING SITE FOR RESIDUE HG B 1195
6	AC6	SOFTWARE	PHE C:759 , CYS C:760 , TYR C:790	BINDING SITE FOR RESIDUE HG C 295
7	AC7	SOFTWARE	CYS C:750 , SER C:752	BINDING SITE FOR RESIDUE HG C 296
8	AC8	SOFTWARE	HOH A:48 , HOH A:126 , LYS A:786 , HG A:1095	BINDING SITE FOR RESIDUE BEZ A 501

(no "SS Bond" information available for 1WSP)

(no "Cis Peptide Bond" information available for 1WSP)

(no "SAP(SNP)/Variant" information available for 1WSP)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIX	PS50841	DIX domain profile.	AXIN1_RAT	745-827	3	A:750-832 B:750-832 C:750-832

(no "Exon" information available for 1WSP)

Asymmetric/Biological 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:83
 aligned with AXIN1_RAT | O70239 from UniProtKB/Swiss-Prot  Length:827

    Alignment length:83
                                   754       764       774       784       794       804       814       824   
            AXIN1_RAT   745 CDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 827
               SCOP domains d1wspa1 A:750-832 Axin 1                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eeeee.....hhhhhhhhh.....eeeeeeee.......eeeeee.............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE DIX  PDB: A:750-832 UniProt: 745-827                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1wsp A 750 CDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 832
                                   759       769       779       789       799       809       819       829

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with AXIN1_RAT | O70239 from UniProtKB/Swiss-Prot  Length:827

    Alignment length:84
                                   753       763       773       783       793       803       813       823    
            AXIN1_RAT   744 PCDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 827
               SCOP domains d1wspb_ B: Axin 1                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeee....hhhhhhhhh.....eeeeeee.........eeeee.............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -DIX  PDB: B:750-832 UniProt: 745-827                                                PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1wsp B 749 PCDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 832
                                   758       768       778       788       798       808       818       828

Chain C from PDB  Type:PROTEIN  Length:84
 aligned with AXIN1_RAT | O70239 from UniProtKB/Swiss-Prot  Length:827

    Alignment length:84
                                   753       763       773       783       793       803       813       823    
            AXIN1_RAT   744 PCDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 827
               SCOP domains d1wspc_ C: Axin 1                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -DIX-1wspC01 C:750-832                                                               Pfam domains (1)
           Pfam domains (2) -DIX-1wspC02 C:750-832                                                               Pfam domains (2)
           Pfam domains (3) -DIX-1wspC03 C:750-832                                                               Pfam domains (3)
         Sec.struct. author ...eeeeeeee......eeeeee....hhhhhhhhh.....eeeeeeee.......eeeeee.............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -DIX  PDB: C:750-832 UniProt: 745-827                                                PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1wsp C 749 PCDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD 832
                                   758       768       778       788       798       808       818       828

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: DIX domain (2)

Protein domain: Axin 1 (2)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d1wspa1	A:750-832
1b	d1wspb_	B:
1c	d1wspc_	C:

(no "CATH Domain" information available for 1WSP)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DIX] (2)

Family: DIX (2)

Rattus norvegicus (Rat) (1)

1a	DIX-1wspC01	C:750-832
1b	DIX-1wspC02	C:750-832
1c	DIX-1wspC03	C:750-832

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (AXIN1_RAT | O70239)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0070016	armadillo repeat domain binding	Interacting selectively and non-covalently with the armadillo repeat domain of a protein, an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity protein armadillo. Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or 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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0030159	receptor signaling complex scaffold activity	Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
biological process
	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:0090244	Wnt signaling pathway involved in somitogenesis	The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state that contributes to somitogenesis.
	GO:0021881	Wnt-activated signaling pathway involved in forebrain neuron fate commitment	The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell that contributes to the commitment of a neuroblast to aneuronal fate. The neuron will reside in the forebrain.
	GO:0007257	activation of JUN kinase activity	The initiation of the activity of the inactive enzyme JUN kinase (JNK).
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0048320	axial mesoderm formation	The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
	GO:0060070	canonical 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, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
	GO:0060823	canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the formation of the neural plate anterior/posterior pattern.
	GO:0008219	cell death	Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
	GO:0071407	cellular response to organic cyclic compound	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 an organic cyclic compound stimulus.
	GO:0031122	cytoplasmic microtubule organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
	GO:0007368	determination of left/right symmetry	The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.
	GO:0009950	dorsal/ventral axis specification	The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
	GO:0048048	embryonic eye morphogenesis	The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
	GO:0060272	embryonic skeletal joint morphogenesis	The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton.
	GO:0021797	forebrain anterior/posterior pattern specification	The creation of specific areas of progenitor domains along the anterior-posterior axis of the developing forebrain.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0055001	muscle cell development	The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.
	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:0090090	negative regulation of canonical Wnt signaling pathway	Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0045599	negative regulation of fat cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
	GO:0034244	negative regulation of transcription elongation from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0030910	olfactory placode formation	The formation of a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity.
	GO:0001743	optic placode formation	The initial developmental process that will lead to the formation of an eye.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:2000060	positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0035412	regulation of catenin import into nucleus	Any process that modulates the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030877	beta-catenin destruction complex	A cytoplasmic protein complex containing glycogen synthase kinase-3-beta (GSK-3-beta), the adenomatous polyposis coli protein (APC), and the scaffolding protein axin, among others; phosphorylates beta-catenin, targets it for degradation by the proteasome.
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005881	cytoplasmic microtubule	Any microtubule in the cytoplasm of a cell.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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.
	GO:0014069	postsynaptic density of dendrite	An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.

Asymmetric/Biological Unit
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	1wsp
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(no "Related Entries Specified in the PDB File" available for 1WSP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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