Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  MOLECULAR MECHANISM OF GUIDANCE CUE RECOGNITION
 
Authors :  Z. Juo, H. Liu, A. Shim, P. Focia, X. Chen, C. Garcia, X. He
Date :  08 Jul 10  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Beta-Propeller, Signaling, Signaling Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Liu, Z. S. Juo, A. H. Shim, P. J. Focia, X. Chen, K. C. Garcia, X. He
Structural Basis Of Semaphorin-Plexin Recognition And Viral Mimicry From Sema7A And A39R Complexes With Plexinc1.
Cell(Cambridge, Mass. ) V. 142 749 2010
PubMed-ID: 20727575  |  Reference-DOI: 10.1016/J.CELL.2010.07.040

(-) Compounds

Molecule 1 - SEMAPHORIN-7A
    Chains: A, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HEK293S
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 45-637
    Gene: SEMA7A, CD108, SEMAL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEMAPHORIN-L, SEMA L, SEMAPHORIN-K1, SEMA K1, JOHN-MILTON- HARGEN HUMAN BLOOD GROUP AG, JMH BLOOD GROUP ANTIGEN, CDW108
 
Molecule 2 - PLEXIN-C1
    Chains: B, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HEK293S
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 33-507
    Gene: PLXNC1, VESPR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VIRUS-ENCODED SEMAPHORIN PROTEIN RECEPTOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1NAG21Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:62 , ASN A:105 , ASP E:185 , ARG E:207BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWAREVAL A:156 , ASN A:157 , HOH A:751 , ASP F:130BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWAREGLN A:223 , ASP A:247 , ASN A:258 , HOH A:698 , HOH A:825BINDING SITE FOR RESIDUE NAG A 3
04AC4SOFTWAREASN A:330 , HIS A:407 , ASP A:432BINDING SITE FOR RESIDUE NDG A 4
05AC5SOFTWAREGLN B:83 , ASN B:86 , THR B:88 , GLU B:89 , PRO B:90BINDING SITE FOR RESIDUE NAG B 1
06AC6SOFTWARELEU B:76 , ASN B:141 , SER B:143BINDING SITE FOR RESIDUE NAG B 2
07AC7SOFTWAREASN B:149 , HOH B:739 , HOH B:740 , HOH B:764BINDING SITE FOR RESIDUE NAG B 3
08AC8SOFTWAREASN B:241 , GLN B:337 , HOH B:741 , HOH B:761BINDING SITE FOR RESIDUE NAG B 4
09AC9SOFTWAREASN B:252 , THR B:254 , SER B:255BINDING SITE FOR RESIDUE NAG B 5
10BC1SOFTWAREASN B:386BINDING SITE FOR RESIDUE NAG B 6
11BC2SOFTWAREASN B:407BINDING SITE FOR RESIDUE NAG B 7
12BC3SOFTWAREASN E:105BINDING SITE FOR RESIDUE NAG E 1
13BC4SOFTWAREVAL E:156 , ASN E:157BINDING SITE FOR RESIDUE NAG E 2
14BC5SOFTWAREGLN E:223 , ASP E:247 , LEU E:257 , ASN E:258 , HOH E:743 , HOH E:802 , HOH E:839BINDING SITE FOR RESIDUE NAG E 3
15BC6SOFTWAREASN E:330 , HIS E:407 , ASP E:432 , HOH E:715BINDING SITE FOR RESIDUE NAG E 4
16BC7SOFTWAREGLN F:83 , ASN F:86 , THR F:88 , GLU F:89 , HOH F:766BINDING SITE FOR RESIDUE NAG F 1
17BC8SOFTWAREGLU A:183 , HIS A:231 , HOH A:818 , ASN F:141BINDING SITE FOR RESIDUE NAG F 2
18BC9SOFTWAREHOH A:842 , ASN F:149 , HOH F:763BINDING SITE FOR RESIDUE NAG F 3
19CC1SOFTWAREASN F:241 , GLN F:337BINDING SITE FOR RESIDUE NAG F 4
20CC2SOFTWAREASN F:252 , SER F:255BINDING SITE FOR RESIDUE NAG F 5
21CC3SOFTWAREASN F:386 , GLU F:406BINDING SITE FOR RESIDUE NAG F 6
22CC4SOFTWAREASN A:582 , GLU F:406 , ASN F:407BINDING SITE FOR RESIDUE NAG F 7

(-) SS Bonds  (34, 34)

Asymmetric/Biological Unit
No.Residues
1A:120 -A:126
2A:143 -A:152
3A:266 -A:366
4A:291 -A:335
5A:493 -A:511
6A:500 -A:541
7A:503 -A:518
8A:566 -A:613
9A:587 -A:596
10B:64 -B:87
11B:156 -B:194
12B:226 -B:354
13B:283 -B:329
14B:455 -B:472
15B:461 -B:506
16B:464 -B:481
17B:475 -B:487
18E:120 -E:126
19E:143 -E:152
20E:266 -E:366
21E:291 -E:335
22E:493 -E:511
23E:500 -E:541
24E:503 -E:518
25E:566 -E:613
26E:587 -E:596
27F:64 -F:87
28F:156 -F:194
29F:226 -F:354
30F:283 -F:329
31F:455 -F:472
32F:461 -F:506
33F:464 -F:481
34F:475 -F:487

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NVQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric/Biological Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029282S115TSEM7A_HUMANPolymorphism16968733A/ES115T
2UniProtVAR_038836R207QSEM7A_HUMANPolymorphism55637216A/ER207Q
3UniProtVAR_038837R207WSEM7A_HUMANPolymorphism56367230A/ER207W
4UniProtVAR_068679R347LSEM7A_HUMANPolymorphism387907241A/ER347L
5UniProtVAR_038838R460HSEM7A_HUMANPolymorphism56204206A/ER460H
6UniProtVAR_038839R461CSEM7A_HUMANPolymorphism56001514A/ER461C
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEMAPS51004 Sema domain profile.SEM7A_HUMAN53-490
 		  2A:53-490
E:53-490

(-) Exons   (0, 0)

(no "Exon" information available for 3NVQ)

(-) 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:588
 aligned with SEM7A_HUMAN | O75326 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:588
                                    55        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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625        
          SEM7A_HUMAN    46 GHLRSGPRIFAVWKGHVGQDRVDFGQTEPHTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGDEVYSTIRKQEYNGKIPRFRRIRGESELYTSDTVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAATNKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDKVFRTSSLKGYHSSLPNPRPGKCLPDQQPIPTETFQVADRHPEVAQRVEPMGPLKTPLFHSKYHYQKVAVHRMQASHGETFHVLYLTTDRGTIHKVVEPGEQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEVSQVPLDLCEVYGGGCHGCLMSRDPYCGWDQGRCISIYSSERSVLQSINPAEPHKECPNPKPDKAPLQKVSLAPNSRYYLSCPMESRHATYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGHYFCEAQEGSYFREAQHWQLLPED 633
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eee........eee......eeeee...eeeeee..........eee.................eeeeeee..eeeeee......eeeee....eeeeee..............eeee..eeee..............eeee....ee.........eeeeeeee...hhhh.eeeeeeeee..........eeeeeeeee..................eeee.............eeeeeeee.....hhhh.eeeeeee.....eeeeeeehhhhhhhhhhh........................hhhhhhhhhhh.................eee...eeeeeeeeee.....eeeeeeeee....eeeee..........eeeeee..........eeeee....eeeee...eeeeee........hhhhhhhhh....eeee..eeee..............................eeeeee.....eeeeee......eeeeee..eeeeee.......eeeeee........eeeeeeee....eeeeeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------T-------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------HC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -------SEMA  PDB: A:53-490 UniProt: 53-490                                                                                                                                                                                                                                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nvq A  46 GHLRSGPRIFAVWKGHVGQDRVDFGQTEPHTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGDEVYSTIRKQEYNGKIPRFRRIRGESELYTSDTVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAATNKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDKVFRTSSLKGYHSSLPNPRPGKCLPDQQPIPTETFQVADRHPEVAQRVEPMGPLKTPLFHSKYHYQKVAVHRMQASHGETFHVLYLTTDRGTIHKVVEPGEQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEVSQVPLDLCEVYGGGCHGCLMSRDPYCGWDQGRCISIYSSERSVLQSINPAEPHKECPNPKPDKAPLQKVSLAPNSRYYLSCPMESRHATYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGHYFCEAQEGSYFREAQHWQLLPED 633
                                    55        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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625        


Chain B from PDB  Type:PROTEIN  Length:474
 aligned with PLXC1_HUMAN | O60486 from UniProtKB/Swiss-Prot  Length:1568

    Alignment length:474
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504    
          PLXC1_HUMAN    35 ADEPVWRSEQAIGAIAASQEDGVFVASGSCLDQLDYSLEHSLSRLYRDQAGNCTEPVSLAPPARPRPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSCHPQGSTAGVVYRAGRNNRWYLAVAATYVLPEPETASRCNPAASDHDTAIALKDTEGRSLATQELGRLKLCEGAGSLHFVDAFLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTEVLFQGQASLDCGHGHPDGRRLLLSSSLVEALDVWAGVFSAAAGEGQERRSPTTTALCLFRMSEIQARAKRVSWDFKTAESHCKEGDQPERVQPIASSTLIHSDLTSVYGTVVMNRTVLFLGTGDGQLLKVILGENLTSNCPEVIYEIKEETPVFYKLVPDPVKNIYIYLTAGKEVRRIRVANCNKHKSCSECLTATDPHCGWCHSLQRCTFQGDCVHSENLENWLDISSGAKKCPK 508
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee......eeee.....eeee...eeeee......eeeeee.........................eeeeeee.........eeeeeehhhhhheeeee.........eee...........eeeeeeee....eeeeeeee...............hhhhh.eeeeeee..hhhhh.....eee......eeee...eee..eeeeeeeeee....ee....eeeeee......eeeeeee...........eeeeeee.hhh.eeeeeee..............eeeeeeehhhhhhhh.....................ee.......eee..eeeeeeee....eeeeeee...eeeeee..........eeeee...........ee......eeeeee..eeeeee..hhhhh.hhhhhhh......eee....eee.............ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nvq B  35 ADEPVWRSEQAIGAIAASQEDGVFVASGSCLDQLDYSLEHSLSRLYRDQAGNCTEPVSLAPPARPRPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSCHPQGSTAGVVYRAGRNNRWYLAVAATYVLPEPETASRCNPAASDHDTAIALKDTEGRSLATQELGRLKLCEGAGSLHFVDAFLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTEVLFQGQASLDCGHGHPDGRRLLLSSSLVEALDVWAGVFSAAAGEGQERRSPTTTALCLFRMSEIQARAKRVSWDFKTAESHCKEGDQPERVQPIASSTLIHSDLTSVYGTVVMNRTVLFLGTGDGQLLKVILGENLTSNCPEVIYEIKEETPVFYKLVPDPVKNIYIYLTAGKEVRRIRVANCNKHKSCSECLTATDPHCGWCHSLQRCTFQGDCVHSENLENWLDISSGAKKCPG 508
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504    


Chain E from PDB  Type:PROTEIN  Length:588
 aligned with SEM7A_HUMAN | O75326 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:588
                                    55        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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625        
          SEM7A_HUMAN    46 GHLRSGPRIFAVWKGHVGQDRVDFGQTEPHTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGDEVYSTIRKQEYNGKIPRFRRIRGESELYTSDTVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAATNKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDKVFRTSSLKGYHSSLPNPRPGKCLPDQQPIPTETFQVADRHPEVAQRVEPMGPLKTPLFHSKYHYQKVAVHRMQASHGETFHVLYLTTDRGTIHKVVEPGEQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEVSQVPLDLCEVYGGGCHGCLMSRDPYCGWDQGRCISIYSSERSVLQSINPAEPHKECPNPKPDKAPLQKVSLAPNSRYYLSCPMESRHATYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGHYFCEAQEGSYFREAQHWQLLPED 633
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------Sema-3nvqE05 E:75-474                                                                                                                                                                                                                                                                                                                                                                                           -----------------------------------------------------------------------Ig_2-3nvqE01 E:546-629                                                              ---- Pfam domains (1)
           Pfam domains (2) -----------------------------Sema-3nvqE06 E:75-474                                                                                                                                                                                                                                                                                                                                                                                           -----------------------------------------------------------------------Ig_2-3nvqE02 E:546-629                                                              ---- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSI-3nvqE03 E:492-550                                      ----------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSI-3nvqE04 E:492-550                                      ----------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ........ee..........eee........eee......eeeee...eeeeee..........eee.................eeeeeee..eeeeee......eeeee.....eeeee..............eeee..eeee..............eeee....ee.........eeeeeeee...hhhh.eeeeeeeee..........eeeeeeeee..................eeee.............eeeeeeee.....hhhh.eeeeeee.....eeeeeeehhhhhhhhhhh........................hhhhhhhhhhh.................eee...eeeeeeeeee.....eeeeeeeee....eeeee..........eeeeee..........eeeee....eeeee...eeeeee........hhhhhhhhh....eeee..eeee..............................eeeeee.....eeeeee......eeeeee..eeeeee.......eeeeee...hhhhheeeeeeee....eeeeeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------T-------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------HC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -------SEMA  PDB: E:53-490 UniProt: 53-490                                                                                                                                                                                                                                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nvq E  46 GHLRSGPRIFAVWKGHVGQDRVDFGQTEPHTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGDEVYSTIRKQEYNGKIPRFRRIRGESELYTSDTVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAATNKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDKVFRTSSLKGYHSSLPNPRPGKCLPDQQPIPTETFQVADRHPEVAQRVEPMGPLKTPLFHSKYHYQKVAVHRMQASHGETFHVLYLTTDRGTIHKVVEPGEQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEVSQVPLDLCEVYGGGCHGCLMSRDPYCGWDQGRCISIYSSERSVLQSINPAEPHKECPNPKPDKAPLQKVSLAPNSRYYLSCPMESRHATYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGHYFCEAQEGSYFREAQHWQLLPED 633
                                    55        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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625        


Chain F from PDB  Type:PROTEIN  Length:474
 aligned with PLXC1_HUMAN | O60486 from UniProtKB/Swiss-Prot  Length:1568

    Alignment length:474
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504    
          PLXC1_HUMAN    35 ADEPVWRSEQAIGAIAASQEDGVFVASGSCLDQLDYSLEHSLSRLYRDQAGNCTEPVSLAPPARPRPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSCHPQGSTAGVVYRAGRNNRWYLAVAATYVLPEPETASRCNPAASDHDTAIALKDTEGRSLATQELGRLKLCEGAGSLHFVDAFLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTEVLFQGQASLDCGHGHPDGRRLLLSSSLVEALDVWAGVFSAAAGEGQERRSPTTTALCLFRMSEIQARAKRVSWDFKTAESHCKEGDQPERVQPIASSTLIHSDLTSVYGTVVMNRTVLFLGTGDGQLLKVILGENLTSNCPEVIYEIKEETPVFYKLVPDPVKNIYIYLTAGKEVRRIRVANCNKHKSCSECLTATDPHCGWCHSLQRCTFQGDCVHSENLENWLDISSGAKKCPK 508
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSI-3nvqF01 F:454-507                                 - Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSI-3nvqF02 F:454-507                                 - Pfam domains (2)
         Sec.struct. author .....ee......eeee.....eeee...eeeee......eeeeee.........................eeeeeee.........eeeeeehhhhhheeeee.........eee...........eeeeeeee....eeeeeeee...............hhhhh.eeeeeee..hhhhh.....eee......eeee...eee..eeeeeeeeee....ee....eeeeee......eeeeeee...........eeeeeeeehhh.eeeeeee..............eeeeeeehhhhhhhh.....................ee.......eee..eeeeeeee....eeeeeee...eeeeee..........eeeee...........ee......eeeeee..eeeeee..hhhhh.hhhhhhh......eee....eee.............ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nvq F  35 ADEPVWRSEQAIGAIAASQEDGVFVASGSCLDQLDYSLEHSLSRLYRDQAGNCTEPVSLAPPARPRPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSCHPQGSTAGVVYRAGRNNRWYLAVAATYVLPEPETASRCNPAASDHDTAIALKDTEGRSLATQELGRLKLCEGAGSLHFVDAFLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTEVLFQGQASLDCGHGHPDGRRLLLSSSLVEALDVWAGVFSAAAGEGQERRSPTTTALCLFRMSEIQARAKRVSWDFKTAESHCKEGDQPERVQPIASSTLIHSDLTSVYGTVVMNRTVLFLGTGDGQLLKVILGENLTSNCPEVIYEIKEETPVFYKLVPDPVKNIYIYLTAGKEVRRIRVANCNKHKSCSECLTATDPHCGWCHSLQRCTFQGDCVHSENLENWLDISSGAKKCPG 508
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
   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 3NVQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NVQ)

(-) Pfam Domains  (3, 8)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: Ig_2 (52)
(-)
Homo sapiens (Human) (39)
1aIg_2-3nvqE01E:546-629
1bIg_2-3nvqE02E:546-629
(-)
Clan: no clan defined [family: PSI] (9)
(-)
Family: PSI (9)
(-)
Homo sapiens (Human) (6)
2aPSI-3nvqF01F:454-507
2bPSI-3nvqF02F:454-507
2cPSI-3nvqE03E:492-550
2dPSI-3nvqE04E:492-550
(-)
Clan: no clan defined [family: Sema] (8)

(-) Gene Ontology  (41, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,E   (SEM7A_HUMAN | O75326)
molecular function
    GO:0045499    chemorepellent activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0038191    neuropilin binding    Interacting selectively and non-covalently with a member of the neuropilin family.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030215    semaphorin receptor binding    Interacting selectively and non-covalently with semaphorin receptors.
biological process
    GO:0048675    axon extension    Long distance growth of a single axon process involved in cellular development.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0050919    negative chemotaxis    The directed movement of a motile cell or organism towards a lower concentration of a chemical.
    GO:0048843    negative regulation of axon extension involved in axon guidance    Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance.
    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:0001755    neural crest cell migration    The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
    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).
    GO:0021988    olfactory lobe development    The progression of the olfactory lobe over time from its initial formation until its mature state. The olfactory lobe is the area of the brain that process the neural inputs for the sense of smell.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0045773    positive regulation of axon extension    Any process that activates or increases the frequency, rate or extent of axon extension.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0060907    positive regulation of macrophage cytokine production    Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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,F   (PLXC1_HUMAN | O60486)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
biological process
    GO:0021785    branchiomotor neuron axon guidance    The process in which a branchiomotor neuron growth cone is directed to a specific target site. Branchiomotor neurons are located in the hindbrain and innervate branchial arch-derived muscles that control jaw movements, facial expression, the larynx, and the pharynx.
    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:0048841    regulation of axon extension involved in axon guidance    Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    GO:1902287    semaphorin-plexin signaling pathway involved in axon guidance    Any semaphorin-plexin signaling pathway that is involved in axon guidance.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    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:0005887    integral component of plasma membrane    The component of the plasma 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.
    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.
    GO:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nvq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3nvq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLXC1_HUMAN | O60486
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SEM7A_HUMAN | O75326
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PLXC1_HUMAN | O60486
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SEM7A_HUMAN | O75326
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLXC1_HUMAN | O60486: 3kuz 3nvn

(-) Related Entries Specified in the PDB File

3nvn 3nvx