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Title :   CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3) IN COMPLEX WITH MOUSE DCC (FN4-5)

Authors :   K. Xu, D. B. Nikolov

Date :   18 May 14 (Deposition) - 18 Jun 14 (Release) - 25 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Elongated, Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Xu, Z. Wu, N. Renier, A. Antipenko, D. Tzvetkova-Robev, Y. Xu, M. Minchenko, V. Nardi-Dei, K. R. Rajashankar, J. Himanen, M. Tessier-Lavigne, D. B. Nikolov
Neural Migration. Structures Of Netrin-1 Bound To Two Receptors Provide Insight Into Its Axon Guidance Mechanism.
Science V. 344 1275 2014
PubMed-ID: 24876346 | Reference-DOI: 10.1126/SCIENCE.1255149

Molecule 1 - NETRIN RECEPTOR DCC
	Chains	:	B
	Fragment	:	FN4-4 (UNP RESIDUES 721-922)
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	TUMOR SUPPRESSOR PROTEIN DCC

Molecule 2 - NETRIN-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Fragment	:	LN-LE3 (UNP RESIDUES 26-457)
	Gene	:	NTN1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:94 , LEU A:95 , ARG A:103	binding site for residue SO4 A 504
2	AC2	SOFTWARE	ARG A:157 , HIS A:209 , HOH A:620 , HOH A:631	binding site for residue SO4 A 505
3	AC3	SOFTWARE	THR A:181 , GLN A:182 , CYS A:183 , ARG A:184 , SER A:191 , ARG A:295 , VAL A:297 , HOH A:602	binding site for residue SO4 A 506
4	AC4	SOFTWARE	ARG A:350 , ARG A:351 , ASN A:372	binding site for residue SO4 A 507
5	AC5	SOFTWARE	GLY A:379 , ARG A:380 , HIS A:383 , TYR A:384	binding site for residue SO4 A 508
6	AC6	SOFTWARE	PHE A:109 , ASP A:112 , THR A:120 , SER A:279 , HOH A:607 , HOH A:619	binding site for residue CA A 509
7	AC7	SOFTWARE	PRO A:76 , ASN A:97 , ASP A:100	binding site for Mono-Saccharide NAG A 501 bound to ASN A 97
8	AC8	SOFTWARE	PRO A:101 , ASN A:118 , LEU A:119 , THR A:120	binding site for Mono-Saccharide NAG A 502 bound to ASN A 118
9	AC9	SOFTWARE	ASN A:133 , TYR A:164 , HOH A:611 , HOH A:614	binding site for Mono-Saccharide NAG A 503 bound to ASN A 133

Asymmetric Unit

No.	Residues
1	A:43	-	A:53
2	A:72	-	A:96
3	A:80	-	A:93
4	A:121	-	A:154
5	A:183	-	A:205
6	A:287	-	A:296
7	A:289	-	A:306
8	A:308	-	A:317
9	A:320	-	A:340
10	A:343	-	A:352
11	A:345	-	A:370
12	A:373	-	A:382
13	A:385	-	A:403
14	A:406	-	A:418
15	A:408	-	A:425
16	A:427	-	A:436
17	A:439	-	A:453

Asymmetric Unit

No.	Residues
1	Tyr A:130	-	Pro A:131
2	Arg A:213	-	Pro A:214
3	Ser A:366	-	Gly A:367
4	Gly A:379	-	Arg A:380

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

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

(no "Exon" information available for 4PLO)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee.......ee........eeeeeeeee..eeeeeeeee..........hhhhhh.........ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee......eeeeeee..hhhhhh................eee...........eeeeee.........hhhhhhhhhhhheeeeeeeeeee......hhhhhhh...eeeeeeeeeee........eee.....eee.....ee.....ee...............................eeehhhhhhhh.....eee......ee.....ee...eee...........eee.........................ee.....ee...eee.......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plo A  40 PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKI 456
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259|      274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454  
                                                                                                                                                                                                                                                     259|                                                                                                                                                                                               
                                                                                                                                                                                                                                                      265

Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee....eeeee...........eeeeeeee.....eeee......eeee.......eeeeeeeeee..ee...eeeeee...hhhhhh.....eeeeeee....eeeeeee.....eeeeeeee.....eeeee...eeeee......eeeeeeeeee..ee......eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plo B 719 GADESQVPDQPSSLHVRPQTNCIIMSWTPPLNPNIVVRGYIIGYGVGSPYAETVRVDSKQRYYSIERLESSSHYVISLKAFNNAGEGVPLYESATTRSITDVSTPMLPPVGVQAVALTHEAVRVSWADNSVRLYTVRWRTSSAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEA 922
                                   728       738       748       758       768       778       788       798       808       818       828       838       848||     867||     880       890       900       910       920  
                                                                                                                                                            849|      868|                                                  
                                                                                                                                                             859       872

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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 4PLO)

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

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

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Asymmetric Unit
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		AC8	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Arg A:213 - Pro A:214	[ RasMol ]
		Gly A:379 - Arg A:380	[ RasMol ]
		Ser A:366 - Gly A:367	[ RasMol ]
		Tyr A:130 - Pro A:131	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	NET1_CHICK \| Q90922
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UniProtKB/Swiss-Prot
	DCC_MOUSE \| P70211	:	3pzd
	NET1_CHICK \| Q90922	:	4plm 4pln

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (17, 17)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (33, 37)

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