3KLD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PTPRG CNTN4 COMPLEX

Authors :   S. Bouyain

Date :   07 Nov 09 (Deposition) - 22 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Cell Adhesion, Protein Complex, Receptor Protein Tyrosine Phosphatase, Neural Recognition Molecule, Glycoprotein, Membrane, Phosphoprotein, Protein Phosphatase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bouyain, D. J. Watkins
The Protein Tyrosine Phosphatases Ptprz And Ptprg Bind To Distinct Members Of The Contactin Family Of Neural Recognition Molecules.
Proc. Natl. Acad. Sci. Usa V. 107 2443 2010
PubMed-ID: 20133774 | Reference-DOI: 10.1073/PNAS.0911235107

Molecule 1 - CONTACTIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PSGHP1
	Expression System Strain	:	HEK293
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	IG DOMAINS 1-4 (UNP RESIDUES 25-404)
	Gene	:	CNTN4
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AXCAM, BIG-2

Molecule 2 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE GAMMA
	Chains	:	B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32
	Expression System Strain	:	ORIGAMI2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CARBONIC ANHYDRASE-LIKE DOMAIN (UNP RESIDUES 55-320)
	Gene	:	PTPRG
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE GAMMA, R-PTP-GAMMA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:64 , ASN A:65 , GLN A:93 , ALA A:95	BINDING SITE FOR RESIDUE NAG A 1001
2	AC2	SOFTWARE	ASN A:191 , HOH A:614	BINDING SITE FOR RESIDUE NAG A 1002
3	AC3	SOFTWARE	PHE A:334 , GLN A:363 , ASN A:370 , HOH A:651	BINDING SITE FOR RESIDUE NAG A 1003
4	AC4	SOFTWARE	ASN A:90	BINDING SITE FOR RESIDUE NAG A 1004

Asymmetric/Biological Unit

No.	Residues
1	A:50	-	A:100
2	A:144	-	A:194
3	A:247	-	A:295
4	A:337	-	A:384
5	B:78	-	B:261

Asymmetric/Biological Unit

No.	Residues
1	Asn A:55	-	Pro A:56
2	Asn A:252	-	Pro A:253
3	Arg A:342	-	Pro A:343
4	Ser B:84	-	Pro B:85
5	Pro B:259	-	Pro B:260

(no "SAP(SNP)/Variant" information available for 3KLD)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	1	B:58-320

(no "Exon" information available for 3KLD)

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:376
 aligned with CNTN4_MOUSE | Q69Z26 from UniProtKB/Swiss-Prot  Length:1026

    Alignment length:380
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
          CNTN4_MOUSE    23 LHGPVFVQEPSHVMFPLDSEEKKVKLSCEVKGNPKPHIRWKINGTDVDIGMDFRYSVVDGSLLINNPNKTQDAGTYQCIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGMVLLCGPPPHSGELSYAWIFNEYPSYQDNRRFVSQETGNLYIAKVEKSDVGNYTCVVTNTVTNHKVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAEKGTTVKLECFALGNPVPTILWRRADGKPIARKARRHKSNGILEIPNFQQEDAGSYECVAENSRGKNVAKGQLTFYAQPNWVQIINDIHVAMEESVFWECKANGRPKPTYRWLKNGDPLLTRDRIQIEQGTLNITIVNLSDAGMYQCVAENKHGVIFSSAELSVI 402
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kldA01 A:23-119 Immunoglobulins                                                                 3kldA02 A:120-221 Immunoglobulins                                                                     3kldA03 A:222-313 Immunoglobulins                                                           ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeee......eeee..eeeee...eeeeee..ee...----.eeee..eeeee..hhhhhheeeeeeeee..eeee...eeeeeeee..........eeeee...eee......ee..eeeeeee..ee......eee......eee...hhhhheeeeeeeee....eeee...eeeeeeeeee...eeeeeeee...eeeee....eeeeeeeeee...eeeeee..........ee.....eeee...hhhhheeeeeeeee..eeeeeeeeeeeeeeeeeee....eeee....eeee.eeeee...eeeeee..ee......eeee..eeee...hhhhheeeeeeeee..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kld A  23 GSGPVFVQEPSHVMFPLDSEEKKVKLSCEVKGNPKPHIRWKLNGTDVDI----RYSVVDGSLLINNPNKTQDAGTYQCIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGMVLLCGPPPHSGELSYAWIFNEYPSYQDNRRFVSQETGNLYIAKVEKSDVGNYTCVVTNTVTNHKVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAEKGTTVKLECFALGNPVPTILWRRADGKPIARKARRHKSNGILEIPNFQQEDAGSYECVAENSRGKNVAKGQLTFYAQPNWVQIINDIHVAMEESVFWECKANGRPKPTYRWLKNGDPLLTRDRIQIEQGTLNITIVNLSDAGMYQCVAENKHGVIFSSAELSVI 402
                                    32        42        52        62        |-   |    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
                                                                           71   76

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with PTPRG_MOUSE | Q05909 from UniProtKB/Swiss-Prot  Length:1442

    Alignment length:265
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315     
          PTPRG_MOUSE    56 GDPYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
               SCOP domains d3kldb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Carb_anhydrase-3kldB01 B:60-320                                                                                                                                                                                                                                       Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh......eehhhhh..---....eee..........eeee....eeee.....eee.......eeeeeeeeee...........ee......eeeeeeee......hhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhh......eee....hhhhhh......eeeeee..........eeeeee...eeeehhhhhhhhh.eeeeee..eeeeee................ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ALPHA_CA_2  PDB: B:58-320 UniProt: 58-321                                                                                                                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kld B  56 GDPYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARV---YQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
                                    65        75        85        95   |   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315     
                                                                  95  99

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: All beta proteins (24004)

Fold: Carbonic anhydrase (525)

Superfamily: Carbonic anhydrase (525)

Family: automated matches (12)

Protein domain: automated matches (12)

Mouse (Mus musculus) [TaxId: 10090] (2)

d3kldb_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	3kldA02	A:120-221
1b	3kldA01	A:23-119
1c	3kldA03	A:222-313

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Carb_anhydrase] (168)

Family: Carb_anhydrase (168)

Mus musculus (Mouse) (6)

Carb_anhydrase-3kldB01

B:60-320

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CNTN4_MOUSE | Q69Z26)

biological process
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	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:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.

Chain B (PTPRG_MOUSE | Q05909)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:1901998	toxin transport	The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:342 - Pro A:343	[ RasMol ]
		Asn A:252 - Pro A:253	[ RasMol ]
		Asn A:55 - Pro A:56	[ RasMol ]
		Pro B:259 - Pro B:260	[ RasMol ]
		Ser B:84 - Pro B:85	[ RasMol ]

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	3kld
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	CNTN4_MOUSE \| Q69Z26
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	PTPRG_MOUSE \| Q05909
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	3.1.3.48
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	CNTN4_MOUSE \| Q69Z26
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	PTPRG_MOUSE \| Q05909
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CNTN4_MOUSE \| Q69Z26	:	3jxa 5e4s
	PTPRG_MOUSE \| Q05909	:	3jxg 5e5u

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

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SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (22, 23)

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