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(-) Description

Title :  MOLECULAR MECHANISM OF GUIDANCE CUE RECOGNITION
 
Authors :  H. Liu, Z. Juo, A. Shim, P. Focia, X. Chen, C. Garcia, X. He
Date :  08 Jul 10  (Deposition) - 15 Sep 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Propeller, Viral Protein (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 - PROTEIN A39
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: HI5
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 15-396
    Gene: A39R
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10249
    Strain: COPENHAGEN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:51 , HOH A:754 , HOH A:823 , TYR B:145 , SER B:202 , LEU B:203 , HIS B:206 , HOH B:483 , HOH B:538 , HOH B:693BINDING SITE FOR RESIDUE NAG A 395
2AC2SOFTWAREASN B:51 , LYS B:52 , THR B:53 , HOH B:633BINDING SITE FOR RESIDUE NAG B 395

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:77 -A:86
2A:118 -A:140
3A:193 -A:287
4A:218 -A:256
5B:77 -B:86
6B:118 -B:140
7B:193 -B:287
8B:218 -B:256

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:281 -Pro A:282
2Ser B:281 -Pro B:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NVX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NVX)

(-) Exons   (0, 0)

(no "Exon" information available for 3NVX)

(-) 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:379
 aligned with SEMA_VACCC | P21062 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:383
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393   
           SEMA_VACCC    14 GIEWHKFETSEEIISTYLLDDVLYTGVNGAVYTFSNNKLNKTGLTNNNYITTSIKVEDADKDTLVCGTNNGNPKCWKIDGSDDPKHRGRGYAPYQNSKVTIISYNECVLSDINISKEGIKRWRRFDGPCGYDLYTADNVIPKDGLRGAFVDKDGTYDKVYILFTDTIGSKRIVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDGRSYRQIIHSRTIKTDNDTILYVFFDSPYSKSALCTYSMNTIKQSFSTSKLEGYTKQLPSPAPGICLPAGKVVSHTTFEVIEKYNVLDDIIKPLSNQPIFEGPSGVKWFDIKEKENEHREYRIYFIKENSIYSFDTKSKQTRSSQVDARLFSVMVTSKPLFIADIGIGVGMPQ 396
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeee..eeeee...eeeeee..eeeeee......eeeeee.----..eeeee.hhhh.eeee.......................eeee..eeee............ee........ee............eeeeeee..eeeeeeeeeeee.....eeeeeeeeee.......hhhhh......eeeee..ee..ee..eeeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhh........................hhhhhhhhhhh.eeeeee.hhhhh..eeee....eeeeee.......eeeeeee..eeeeee.....eeeee....eeeeee...eeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nvx A  12 SIEWHKFETSEEIISTYLLDDVLYTGVNGAVYTFSNNKLNKTGLTNNNYITTSIKV----KDTLVCGTNNGNPKCWKIDGSDDPKHRGRGYAPYQNSKVTIISYNECVLSDINISKEGIKRWRRFDGPCGYDLYTADNVIPKDGLRGAFVDKDGTYDKVYILFTDTIGSKRIVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDGRSYRQIIHSRTIKTDNDTILYVFFDSPYSKSALCTYSMNTIKQSFSTSKLEGYTKQLPSPAPGICLPAGKVVSHTTFEVIEKYNVLDDIIKPLSNQPIFEGPSGVKWFDIKEKENEHREYRIYFIKENSIYSFDTKSKQTRSSQVDARLFSVMVTSKPLFIADIGIGVGMPQ 394
                                    21        31        41        51        61     |   -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391   
                                                                                  67   72                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with SEMA_VACCC | P21062 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:381
                                    24        34        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 
           SEMA_VACCC    15 IEWHKFETSEEIISTYLLDDVLYTGVNGAVYTFSNNKLNKTGLTNNNYITTSIKVEDADKDTLVCGTNNGNPKCWKIDGSDDPKHRGRGYAPYQNSKVTIISYNECVLSDINISKEGIKRWRRFDGPCGYDLYTADNVIPKDGLRGAFVDKDGTYDKVYILFTDTIGSKRIVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDGRSYRQIIHSRTIKTDNDTILYVFFDSPYSKSALCTYSMNTIKQSFSTSKLEGYTKQLPSPAPGICLPAGKVVSHTTFEVIEKYNVLDDIIKPLSNQPIFEGPSGVKWFDIKEKENEHREYRIYFIKENSIYSFDTKSKQTRSSQVDARLFSVMVTSKPLFIADIGIGVGMP 395
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeeee..eeeeee..eeeeee..eeeeee......eeeee.------..eeee......eeee.......................eeee..eeee............ee........ee............eeeeeee..eeeeeeeeeeee.....eeeeeeeeee..................eeeee..ee..ee..eeeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhh........................hhhhhhhhhhh.eeeeee.hhhhh..eeee....eeeeee.----..eeeeeee..eeeeee.....eeeee....eeeeee...eeeee..eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nvx B  13 IEWHKFETSEEIISTYLLDDVLYTGVNGAVYTFSNNKLNKTGLTNNNYITTSIK------DTLVCGTNNGNPKCWKIDGSDDPKHRGRGYAPYQNSKVTIISYNECVLSDINISKEGIKRWRRFDGPCGYDLYTADNVIPKDGLRGAFVDKDGTYDKVYILFTDTIGSKRIVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDGRSYRQIIHSRTIKTDNDTILYVFFDSPYSKSALCTYSMNTIKQSFSTSKLEGYTKQLPSPAPGICLPAGKVVSHTTFEVIEKYNVLDDIIKPLSNQPIFEGPSGVKWFDIKEK----REYRIYFIKENSIYSFDTKSKQTRSSQVDARLFSVMVTSKPLFIADIGIGVGMP 393
                                    22        32        42        52        62   |     -|       82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  |    342       352       362       372       382       392 
                                                                                66     73                                                                                                                                                                                                                                                                   335  340
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3NVX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NVX)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SEMA_VACCC | P21062)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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3nvn 3nvq