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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3) COMPLEXED WITH MOUSE NEOGENIN (FN4-5)
 
Authors :  K. Xu, D. B. Nikolov
Date :  18 May 14  (Deposition) - 18 Jun 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Elongated, Cysteine Rich, Glycoprotein, 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

(-) Compounds

Molecule 1 - NETRIN-1
    Chains: A, B
    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
 
Molecule 2 - NEOGENIN
    Chains: C, D
    Fragment: FN4-5 (UNP RESIDUES 765-964)
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:109 , ASP A:112 , THR A:120 , SER A:279binding site for residue CA A 504
2AC2SOFTWAREPHE B:109 , ASP B:112 , THR B:120 , SER B:279binding site for residue CA B 504
3AC3SOFTWAREASN A:97 , SER A:99binding site for Mono-Saccharide NAG A 501 bound to ASN A 97
4AC4SOFTWAREPRO A:101 , ASN A:118 , LEU A:119binding site for Mono-Saccharide NAG A 502 bound to ASN A 118
5AC5SOFTWAREPRO A:131 , ASN A:133 , SER A:254binding site for Mono-Saccharide NAG A 503 bound to ASN A 133
6AC6SOFTWAREPRO B:76 , LEU B:95 , ASN B:97 , SER B:99 , ASP B:100binding site for Mono-Saccharide NAG B 501 bound to ASN B 97
7AC7SOFTWAREPRO B:101 , PHE B:109 , ASN B:118 , LEU B:119binding site for Mono-Saccharide NAG B 502 bound to ASN B 118
8AC8SOFTWAREPRO B:131 , HIS B:132 , ASN B:133 , SER B:254binding site for Mono-Saccharide NAG B 503 bound to ASN B 133

(-) SS Bonds  (34, 34)

Asymmetric/Biological Unit
No.Residues
1A:43 -A:53
2A:72 -A:96
3A:80 -A:93
4A:121 -A:154
5A:183 -A:205
6A:287 -A:296
7A:289 -A:306
8A:308 -A:317
9A:320 -A:340
10A:343 -A:352
11A:345 -A:370
12A:373 -A:382
13A:385 -A:403
14A:406 -A:418
15A:408 -A:425
16A:427 -A:436
17A:439 -A:453
18B:43 -B:53
19B:72 -B:96
20B:80 -B:93
21B:121 -B:154
22B:183 -B:205
23B:287 -B:296
24B:289 -B:306
25B:308 -B:317
26B:320 -B:340
27B:343 -B:352
28B:345 -B:370
29B:373 -B:382
30B:385 -B:403
31B:406 -B:418
32B:408 -B:425
33B:427 -B:436
34B:439 -B:453

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1His A:47 -Gly A:48
2Lys A:74 -Pro A:75
3Tyr A:130 -Pro A:131
4Val A:212 -Arg A:213
5Arg A:213 -Pro A:214
6His B:47 -Gly B:48
7Tyr B:130 -Pro B:131
8Arg B:213 -Pro B:214
9Ile C:914 -Pro C:915
10Pro D:864 -Asp D:865
11Ile D:914 -Pro D:915

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLN)

(-) Sequences/Alignments

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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee.......ee........eeeeeeee....eeeeeeee.........................ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee.hhhhhhh................ee............eeeee......hhhhhhhhhhhhhhheeeeeeeeeee...........hhhhhh....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
                 4pln A  40 PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKI 456
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       


Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee.......ee........eeeeeeeee..eeeeeeeee..........hhhhhh.........ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee.hhhhhhh................ee............eeeee......hhhhhhhhhhhhhhheeeeeeeeeee...........hhhhhh....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
                 4pln B  40 PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKI 456
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeeeee........eeeeeeee.....eeeeee....eeee.......eeeeeeeeee..ee...eeeeee...............eeeeeee.....eeeeee.............eeeeeeeee........eeeee...eeee.......eeeeeeeeee..ee......eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pln C 763 GSDETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNAQATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATASG 967
                                   772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962     


Chain D from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeee....eeeeee..........eeeeeeee.....eeeeee....eeee.......eeeeeeeeee..ee...eeeeee...............eeeeeee.....eeeeee.............eeeeeeeee........eeeee...eeee.......eeeeeeeeee..ee......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pln D 763 GSDETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNAQATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATAS 966
                                   772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PLN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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  4pln
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  NET1_CHICK | Q90922
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NEO1_MOUSE | P97798: 4bq6 4bq7 4bq8 4bq9 4bqb 4bqc 4ui2
        NET1_CHICK | Q90922: 4plm 4plo

(-) Related Entries Specified in the PDB File

4plm 4plo