1WWC - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   NT3 BINDING DOMAIN OF HUMAN TRKC RECEPTOR

Authors :   M. H. Ultsch, C. Wiesmann, L. C. Simmons, J. Henrich, M. Yang, D. Reilly, A. M. De Vos

Date :   30 Apr 99 (Deposition) - 07 Jul 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Trk Receptor, Receptor Tyrosine Kinase, 3D-Domain Swapping, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Ultsch, C. Wiesmann, L. C. Simmons, J. Henrich, M. Yang, D. Reilly S. H. Bass, A. M. De Vos
Crystal Structures Of The Neurotrophin-Binding Domain Of Trka, Trkb And Trkc.
J. Mol. Biol. V. 290 149 1999
PubMed-ID: 10388563 | Reference-DOI: 10.1006/JMBI.1999.2816

Molecule 1 - PROTEIN (NT-3 GROWTH FACTOR RECEPTOR TRKC)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	LIGAND BINDING DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1WWC)

(no "Site" information available for 1WWC)

Asymmetric Unit

No.	Residues
1	A:320	-	A:362

Asymmetric Unit

No.	Residues
1	Asn A:328	-	Pro A:329

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041472	R	306	C	NTRK3_HUMAN	Polymorphism	56386352	A	R	306	C
2	UniProt	VAR_041473	V	307	L	NTRK3_HUMAN	Unclassified	---	A	V	307	L
3	UniProt	VAR_041474	L	336	Q	NTRK3_HUMAN	Unclassified	---	A	L	336	Q

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041472	R	306	C	NTRK3_HUMAN	Polymorphism	56386352	A	R	306	C
2	UniProt	VAR_041473	V	307	L	NTRK3_HUMAN	Unclassified	---	A	V	307	L
3	UniProt	VAR_041474	L	336	Q	NTRK3_HUMAN	Unclassified	---	A	L	336	Q

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

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041472	R	306	C	NTRK3_HUMAN	Polymorphism	56386352	A	R	306	C
2	UniProt	VAR_041473	V	307	L	NTRK3_HUMAN	Unclassified	---	A	V	307	L
3	UniProt	VAR_041474	L	336	Q	NTRK3_HUMAN	Unclassified	---	A	L	336	Q

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

(no "PROSITE Motif" information available for 1WWC)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000360948	2b	ENSE00001400416	chr15:88799661-88799515	147	NTRK3_HUMAN	-	0	0	-	-
1.3	ENST00000360948	3	ENSE00002158319	chr15:88799399-88799137	263	NTRK3_HUMAN	1-83	83	0	-	-
1.4	ENST00000360948	4	ENSE00001696452	chr15:88727530-88727456	75	NTRK3_HUMAN	83-108	26	0	-	-
1.5	ENST00000360948	5	ENSE00001608071	chr15:88726720-88726649	72	NTRK3_HUMAN	108-132	25	0	-	-
1.6	ENST00000360948	6	ENSE00001700495	chr15:88690634-88690566	69	NTRK3_HUMAN	132-155	24	0	-	-
1.7	ENST00000360948	7	ENSE00001796940	chr15:88680792-88680635	158	NTRK3_HUMAN	155-208	54	0	-	-
1.8	ENST00000360948	8	ENSE00001663999	chr15:88679840-88679698	143	NTRK3_HUMAN	208-255	48	0	-	-
1.9	ENST00000360948	9	ENSE00001741518	chr15:88679271-88679130	142	NTRK3_HUMAN	256-303	48	1	A:300-303	4
1.10	ENST00000360948	10	ENSE00001805730	chr15:88678628-88678332	297	NTRK3_HUMAN	303-402	100	1	A:303-401	99
1.11	ENST00000360948	11	ENSE00001766954	chr15:88671965-88671942	24	NTRK3_HUMAN	402-410	9	1	A:402-402	1
1.12	ENST00000360948	12	ENSE00001754979	chr15:88670457-88670393	65	NTRK3_HUMAN	410-431	22	1	A:402-404	3
1.13	ENST00000360948	13	ENSE00001595872	chr15:88669604-88669502	103	NTRK3_HUMAN	432-466	35	0	-	-
1.14	ENST00000360948	14	ENSE00001654221	chr15:88576276-88576088	189	NTRK3_HUMAN	466-529	64	0	-	-
1.17	ENST00000360948	17	ENSE00001134154	chr15:88483984-88483854	131	NTRK3_HUMAN	529-572	44	0	-	-
1.18	ENST00000360948	18	ENSE00000943684	chr15:88476415-88476243	173	NTRK3_HUMAN	573-630	58	0	-	-
1.20	ENST00000360948	20	ENSE00000943685	chr15:88472665-88472422	244	NTRK3_HUMAN	630-711	82	0	-	-
1.21	ENST00000360948	21	ENSE00000943688	chr15:88428966-88428925	42	NTRK3_HUMAN	712-725	14	0	-	-
1.22	ENST00000360948	22	ENSE00001766468	chr15:88423659-88423501	159	NTRK3_HUMAN	726-778	53	0	-	-
1.23a	ENST00000360948	23a	ENSE00001134128	chr15:88420351-88420022	330	NTRK3_HUMAN	779-839	61	0	-	-

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:105
 aligned with NTRK3_HUMAN | Q16288 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:113
                                   309       319       329       339       349       359       369       379       389       399       409   
          NTRK3_HUMAN   300 TVYYPPRVVSLEEPELRLEHCIEFVVRGNPPPTLHWLHNGQPLRESKIIHVEYYQEGEISEGCLLFNKPTHYNNGNYTLIAKNPLGTANQTINGHFLKEPFPESTDNFILFDE 412
               SCOP domains d1wwca_ A: NT3 binding domain of trkC receptor                                                                    SCOP domains
               CATH domains 1wwcA00 A:300-404 Immunoglobulins                                                                                 CATH domains
               Pfam domains -----------------I-set-1wwcA01 A:317-392                                                     -------------------- Pfam domains
         Sec.struct. author ..................eeeeeeeee.....eeeeee..........eeeeeee...eeeeeeeee...hhh.eeeeeeeee..eeeeeeeee........--------... Sec.struct. author
                 SAPs(SNPs) ------CL----------------------------Q---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---Exon 1.10  PDB: A:303-401 UniProt: 303-402 [INCOMPLETE]                                             -------1.1 Transcript 1 (1)
           Transcript 1 (2) 1.9 --------------------------------------------------------------------------------------------------Exon 1.11-- Transcript 1 (2)
                 1wwc A 300 TVYYPPRVVSLEEPELRLEHCIEFVVRGNPPPTLHWLHNGQPLRESKIIHVEYYQEGEISEGCLLFNKPTHYNNGNYTLIAKNPLGTANQTINGHFLKEPFP--------VDE 404
                                   309       319       329       339       349       359       369       379       389       399 |       -|  
                                                                                                                               401      402

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(

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Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: I set domains (152)

Protein domain: NT3 binding domain of trkC receptor (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1wwca_

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1wwcA00

A:300-404

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

I-set-1wwcA01

A:317-392

Asymmetric Unit(hide GO term definitions)

Chain A (NTRK3_HUMAN | Q16288)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005004	GPI-linked ephrin receptor activity	Combining with a GPI-anchored ephrin to initiate a change in cell activity.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0043121	neurotrophin binding	Interacting selectively and non-covalently with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth.
	GO:0005030	neurotrophin receptor activity	Combining with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth, and transmitting the signal to initiate a change in cell activity.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of 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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0004714	transmembrane receptor protein tyrosine kinase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
	GO:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0032148	activation of protein kinase B activity	Any process that initiates the activity of the inactive enzyme protein kinase B.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0071300	cellular response to retinoic acid	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 retinoic acid stimulus.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0090102	cochlea development	The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0070306	lens fiber cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
	GO:0042490	mechanoreceptor differentiation	The process in which a relatively unspecialized cell acquires specialized features of a mechanoreceptor, a cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
	GO:0019056	modulation by virus of host transcription	Any process in which a virus modulates the frequency, rate or extent of its host's transcription.
	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:0048712	negative regulation of astrocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
	GO:0060548	negative regulation of cell death	Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0048665	neuron fate specification	The process in which a cell becomes capable of differentiating autonomously into a neuron in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.
	GO:0001764	neuron migration	The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
	GO:0038179	neurotrophin signaling pathway	A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:2000251	positive regulation of actin cytoskeleton reorganization	Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0048691	positive regulation of axon extension involved in regeneration	Any process that activates, maintains or increases the rate of axon extension involved in regeneration.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0050927	positive regulation of positive chemotaxis	Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0051965	positive regulation of synapse assembly	Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048678	response to axon injury	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an axon injury stimulus.
	GO:0051412	response to corticosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a corticosterone stimulus. Corticosterone is a 21 carbon steroid hormone of the corticosteroid type, produced in the cortex of the adrenal glands. In many species, corticosterone is the principal glucocorticoid, involved in regulation of fuel metabolism, immune reactions, and stress responses.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005887	integral component of plasma membrane	The component of the plasma 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: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:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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(no "Ligands, Modified Residues, Ions" information available for 1wwc)

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(no "Sites" information available for 1wwc)

	Cis Peptide Bonds
		Asn A:328 - Pro A:329	[ RasMol ]

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	1wwc
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	NTRK3_HUMAN \| Q16288
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	NTRK3_HUMAN \| Q16288	:	3v5q 4ymj

1wwa	TRKA
1wwb	TRKB

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (3, 3)

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Exons (4, 4)

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