4PBV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CHICKEN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA IN COMPLEX WITH TRKC

Authors :   C. H. Coles, N. Mitakidis, P. Zhang, J. Elegheert, W. Lu, A. W. Stoker, T. A. M. Craig, E. Y. Jones, A. R. Aricescu

Date :   14 Apr 14 (Deposition) - 12 Nov 14 (Release) - 19 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: E  (1x)

Keywords :   Signaling Protein, Synapse Cell Signalling Cell Surface Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Coles, N. Mitakidis, P. Zhang, J. Elegheert, W. Lu, A. W. Stoker, T. Nakagawa, A. M. Craig, E. Y. Jones, A. R. Aricescu
Structural Basis For Extracellular Cis And Trans Rptp Sigma Signal Competition In Synaptogenesis.
Nat Commun V. 5 5209 2014
PubMed-ID: 25385546 | Reference-DOI: 10.1038/NCOMMS6209

Molecule 1 - NT-3 GROWTH FACTOR RECEPTOR
	Chains	:	A, B
	EC Number	:	2.7.10.1
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 31-302
	Gene	:	NTRK3, TRKC
	Mutation	:	YES
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 3,TRKC TYROSINE KINASE,TRK-C

Molecule 2 - PROTEIN-TYROSINE PHOSPHATASE CRYPALPHA1 ISOFORM
	Chains	:	C, D, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 29-316
	Gene	:	CRYPALPHA1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	IG3 DOMAIN IS NOT VISIBLE IN ELECTRON DENSITY, SUGGESTING THAT THIS DOMAIN HAD EITHER BEEN PROTEOLYTICALLY CLEAVED DURING CRYSTALLISATION OR IS DISORDERED.

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:237 , ASN D:73 , HOH D:501 , ARG E:227	binding site for residue SO4 D 401
2	AC2	SOFTWARE	SER E:74 , ARG E:76 , ARG E:96 , ARG E:99 , HOH E:511	binding site for residue SO4 E 401
3	AC3	SOFTWARE	ASP A:61 , ASN A:79 , PRO D:140 , GLN D:141 , SER D:218 , PRO D:219	binding site for Mono-Saccharide NAG A 401 bound to ASN A 79
4	AC4	SOFTWARE	ASN A:203 , THR A:205	binding site for Mono-Saccharide NAG A 403 bound to ASN A 203
5	AC5	SOFTWARE	ASN A:272	binding site for Mono-Saccharide NAG A 402 bound to ASN A 272
6	AC6	SOFTWARE	ASP B:61 , ASN B:79 , SER C:218	binding site for Mono-Saccharide NAG B 401 bound to ASN B 79
7	AC7	SOFTWARE	ASN B:272	binding site for Mono-Saccharide NAG B 402 bound to ASN B 272

Asymmetric Unit

No.	Residues
1	A:32	-	A:38
2	A:36	-	A:45
3	A:164	-	A:189
4	A:166	-	A:207
5	A:231	-	A:284
6	B:32	-	B:38
7	B:36	-	B:45
8	B:164	-	B:189
9	B:166	-	B:207
10	B:231	-	B:284
11	C:53	-	C:106
12	C:155	-	C:206
13	D:53	-	D:106
14	D:155	-	D:206
15	E:53	-	E:106
16	E:155	-	E:206

Asymmetric Unit

No.	Residues
1	Ser A:236	-	Pro A:237
2	Ser B:236	-	Pro B:237
3	Asp C:58	-	Pro C:59
4	Gln C:93	-	Pro C:94
5	Thr C:97	-	Pro C:98
6	Asn C:160	-	Pro C:161
7	Ser C:179	-	Asn C:180
8	Asp D:58	-	Pro D:59
9	Gln D:93	-	Pro D:94
10	Thr D:97	-	Pro D:98
11	Asn D:160	-	Pro D:161
12	Asp E:58	-	Pro E:59
13	Gln E:93	-	Pro E:94
14	Thr E:97	-	Pro E:98
15	Asn E:160	-	Pro E:161

(no "SAP(SNP)/Variant" information available for 4PBV)

(no "PROSITE Motif" information available for 4PBV)

(no "Exon" information available for 4PBV)

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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee..............hhhhh..eeeee.........hhhh.......eeeee...................eee..........hhhh......eee.........hhhhhhhhhhhh..........eee.....eee............eeee...eeeee....eeeeeeee.....eeee.......eeeeee..eeeeeeeee.........eeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbv A  29 ETGCPANCLCSKTDINCKKPDDGNLFPLLEGQDSRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVYGT 304
                                    38        48        58   ||   83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   ||  267       277       287       297       
                                                            62|                                                                                                                                                                                257|                                          
                                                             78                                                                                                                                                                                 262

Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..............hhhhh..eeeee.........hhhh.......eeeee...................eee..........hhhh......eee.........hhhhhhhhhhhh..........eee.....eee............eeee...eeeee....eeeeeeee.....eeee.......eeeeee..eeeeeeeee.........eeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbv B  31 GCPANCLCSKTDINCKKPDDGNLFPLLEGQDSRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVYG 303
                                    40        50        60 ||     85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 ||    269       279       289       299    
                                                          62|                                                                                                                                                                                257|                                         
                                                           78                                                                                                                                                                                 262

Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee.....eeeee......eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee.............eee.....eee........eeeeeeeee..eeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbv C  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNKVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRVR 227
                                    38        48        58        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
                                                                 67|                                                                                                                                                           
                                                                  72

Chain D from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee.....eeeee.......eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee..eee........eee.....eee........eeeeeeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbv D  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNKKVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRV 226
                                    38        48        58        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
                                                                 67|                                                                                                                                                           
                                                                  71

Chain E from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee.....eeeee....eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee.............eee.....eee........eeeeeeeee..eeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbv E  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNKSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRVRR 228
                                    38        48        58        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                 67|                                                                                                                                                          
                                                                  74

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4PBV)

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

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

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	Cis Peptide Bonds
		Asn C:160 - Pro C:161	[ RasMol ]
		Asn D:160 - Pro D:161	[ RasMol ]
		Asn E:160 - Pro E:161	[ RasMol ]
		Asp C:58 - Pro C:59	[ RasMol ]
		Asp D:58 - Pro D:59	[ RasMol ]
		Asp E:58 - Pro E:59	[ RasMol ]
		Gln C:93 - Pro C:94	[ RasMol ]
		Gln D:93 - Pro D:94	[ RasMol ]
		Gln E:93 - Pro E:94	[ RasMol ]
		Ser A:236 - Pro A:237	[ RasMol ]
		Ser B:236 - Pro B:237	[ RasMol ]
		Ser C:179 - Asn C:180	[ RasMol ]
		Thr C:97 - Pro C:98	[ RasMol ]
		Thr D:97 - Pro D:98	[ RasMol ]
		Thr E:97 - Pro E:98	[ RasMol ]

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2yd4	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF CHICKEN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (16, 16)

Cis Peptide Bonds (15, 15)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (36, 47)

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