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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH FN5-FN6 OF DCC
 
Authors :  L. I. Finci, N. Krueger, X. Sun, J. Zhang, M. Chegkazi, Y. Wu, G. Schenk, H. D. T. Mertens, D. I. Svergun, Y. Zhang, J. -H. Wang, R. Meijers
Date :  02 Jul 14  (Deposition) - 10 Sep 14  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (2x)
Keywords :  Protein Binding, Apoptosis, Axon Guidance, Dependence Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. I. Finci, N. Krueger, X. Sun, J. Zhang, M. Chegkazi, Y. Wu, G. Schenk, H. D. T. Mertens, D. I. Svergun, Y. Zhang, J. -H. Wang, R. Meijers
The Crystal Structure Of Netrin-1 In Complex With Dcc Reveals The Bi-Functionality Of Netrin-1 As A Guidance Cue
Neuron V. 83 839 2014
PubMed-ID: 25123307  |  Reference-DOI: 10.1016/J.NEURON.2014.07.010

(-) Compounds

Molecule 1 - NETRIN-1
    Chains: A
    Fragment: VI AND V DOMAINS, RESIDUES 39-453
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPIDIDYMIS TISSUE PROTEIN LI 131P
 
Molecule 2 - NETRIN RECEPTOR DCC
    Chains: B
    Fragment: FN5-FN6, RESIDUES 844-1043
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COLORECTAL CANCER SUPPRESSOR, IMMUNOGLOBULIN SUPERFAMILY DCC SUBCLASS MEMBER 1, TUMOR SUPPRESSOR PROTEIN DCC, DELETED IN COLORECTAL CANCER

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A (1x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric Unit (5, 26)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO417Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:107 , ASP A:110 , ASN A:112 , THR A:118 , SER A:277BINDING SITE FOR RESIDUE CA A1465
02AC2SOFTWAREARG A:317 , CYS A:318 , LYS A:319 , PRO A:320 , TYR A:323 , THR B:856 , ASP B:858BINDING SITE FOR RESIDUE CL A1466
03AC3SOFTWARETRP A:171 , ARG A:248BINDING SITE FOR RESIDUE SO4 A1467
04AC4SOFTWAREASP A:224 , GLY A:225 , ASP A:427 , SO4 A:1481BINDING SITE FOR RESIDUE SO4 A1468
05AC5SOFTWAREARG A:155 , HIS A:207 , ASP A:209BINDING SITE FOR RESIDUE SO4 A1469
06AC6SOFTWAREARG A:307 , HIS A:308 , ASN A:309BINDING SITE FOR RESIDUE SO4 A1470
07AC7SOFTWAREARG A:349 , ASN A:370BINDING SITE FOR RESIDUE SO4 A1471
08AC8SOFTWAREGLY A:431 , ILE A:432 , ARG A:436BINDING SITE FOR RESIDUE SO4 A1472
09AC9SOFTWARECYS A:437 , TYR A:441 , THR B:934 , ALA B:935 , HIS B:936BINDING SITE FOR RESIDUE SO4 A1473
10BC1SOFTWAREARG A:349 , ARG A:351 , SO4 A:1477 , GLY B:909 , TYR B:916BINDING SITE FOR RESIDUE SO4 A1474
11BC2SOFTWARETYR A:162 , ARG A:248 , NAG A:1463BINDING SITE FOR RESIDUE SO4 A1475
12BC3SOFTWAREGLY A:377 , ARG A:378 , HIS A:381BINDING SITE FOR RESIDUE SO4 A1476
13BC4SOFTWAREASN A:370 , SO4 A:1474BINDING SITE FOR RESIDUE SO4 A1477
14BC5SOFTWARETHR A:430 , ARG A:436 , ALA A:438 , LYS A:439BINDING SITE FOR RESIDUE SO4 A1478
15BC6SOFTWAREARG A:348 , ARG A:372 , HIS A:373 , ARG A:398BINDING SITE FOR RESIDUE SO4 A1479
16BC7SOFTWAREARG A:182 , ASN A:186 , PRO A:188 , SO4 A:1483BINDING SITE FOR RESIDUE SO4 A1480
17BC8SOFTWARELYS A:426 , ASP A:427 , SO4 A:1468BINDING SITE FOR RESIDUE SO4 A1481
18BC9SOFTWARESO4 A:1480BINDING SITE FOR RESIDUE SO4 A1483
19CC1SOFTWAREARG A:317 , THR B:906BINDING SITE FOR RESIDUE SO4 B2051
20CC2SOFTWAREALA B:854 , THR B:938BINDING SITE FOR RESIDUE GOL B2052
21CC3SOFTWAREPRO A:74 , ASN A:95 , SER A:97 , ASP A:98BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1459 THROUGH NAG A1460 BOUND TO ASN A 95
22CC4SOFTWAREASN A:131 , TYR A:162 , SO4 A:1475BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1463 THROUGH NAG A1464 BOUND TO ASN A 131
23CC5SOFTWARELYS A:100 , ASN A:116BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1461 THROUGH NAG A1462

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:41 -A:51
2A:70 -A:94
3A:78 -A:91
4A:119 -A:152
5A:181 -A:203
6A:285 -A:294
7A:287 -A:304
8A:306 -A:315
9A:318 -A:338
10A:341 -A:350
11A:343 -A:368
12A:371 -A:380
13A:383 -A:401
14A:404 -A:416
15A:406 -A:423
16A:425 -A:434
17A:437 -A:451

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Asn A:45 -Gly A:46
2Arg A:72 -Pro A:73
3Glu A:123 -Asn A:124
4Phe A:128 -Pro A:129
5Asn B:872 -Gln B:873
6Lys B:874 -Thr B:875
7Asn B:925 -Arg B:926
8Glu B:957 -Gly B:958
9Phe B:1049 -Ala B:1050

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4URT)

(-) Sequences/Alignments

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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................ee.................eeeee..........eeeee.........hhhhh...........ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee.hhhhhh..........hhhhh.eee............eeeee....hhhhhhhhhhhhhhhhheeeeeeeee................hhhhh..eeeeeeeeeee........eee.....eee.....ee.....ee..............................eeeehhhhhhhh.....eeee.....ee.....ee...eee...........eee.........................ee.....ee...ee..........ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4urt A   39 DPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKELHHH  458
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeee..............eeeeeeee...........ee...eeee.......eeeeeeeeee..ee......eeee..........eeeeeee.......eeeeee..........eeeeeee............eee.....eeee.......eeeeeeeeee..ee........ee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4urt B  844 MLPPVGVQAVALTHDAVRVSWADNSVPKNQKTSEVRLYTVRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKLEVLFA 1050
                                   853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043|     
                                                                                                                                                                                                                                1043|     
                                                                                                                                                                                                                                 1045
   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 4URT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 46)

Asymmetric Unit(hide GO term definitions)

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  4urt
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 Related Entries

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        DCC_HUMAN | P43146: 2ed7 2ed8 2ed9 2edb 2edd 2ede 3au4

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