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(-) Description

Title :  PARAINFLUENZA VIRUS 5 (SV5) HEMAGGLUTININ-NEURAMINIDASE (HN) WITH LIGAND DANA (SOAKED WITH DANA, PH 7.0)
 
Authors :  P. Yuan, T. B. Thompson, B. A. Wurzburg, R. G. Paterson, R. A. Lamb, T. S. J
Date :  16 Mar 05  (Deposition) - 24 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Keywords :  Hemagglutinin, Neuraminidase, Fusion, Tetramer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Yuan, T. B. Thompson, B. A. Wurzburg, R. G. Paterson, R. A. Lamb, T. S. Jardetzky
Structural Studies Of The Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Tetramer In Complex With Its Receptor, Sialyllactose.
Structure V. 13 803 2005
PubMed-ID: 15893670  |  Reference-DOI: 10.1016/J.STR.2005.02.019

(-) Compounds

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
    ChainsA
    EC Number3.2.1.18
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPBACGUS-3
    Expression System Taxid7111
    Expression System Vector TypeVIRUS
    FragmentEXTRACELLULAR DOMAIN
    GeneHN
    Organism ScientificSIMIAN VIRUS 5
    Organism Taxid11207
    StrainW3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DAN4Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:139BINDING SITE FOR RESIDUE NDG A 1
2AC2SOFTWARENAG A:3 , ASN A:267 , THR A:269 , GLN A:369BINDING SITE FOR RESIDUE NAG A 2
3AC3SOFTWARENAG A:2 , GLN A:369BINDING SITE FOR RESIDUE NAG A 3
4AC4SOFTWARENAG A:5 , GLU A:481 , ASN A:504 , THR A:506 , GLN A:507 , ILE A:509BINDING SITE FOR RESIDUE NAG A 4
5AC5SOFTWARENAG A:4 , GLN A:507BINDING SITE FOR RESIDUE NAG A 5
6AC6SOFTWAREASP A:250 , SER A:253 , ALA A:255 , ALA A:285 , HOH A:703BINDING SITE FOR RESIDUE CA A 600
7AC7SOFTWAREARG A:163 , GLU A:247 , ASN A:288 , TYR A:306 , GLU A:390 , ARG A:405 , ASN A:407 , ARG A:495 , TYR A:523 , HOH A:619 , HOH A:645 , HOH A:666 , HOH A:706 , HOH A:732 , HOH A:742 , HOH A:811BINDING SITE FOR RESIDUE DAN A 601

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:161 -A:185
2A:175 -A:236
3A:227 -A:240
4A:365 -A:375
5A:448 -A:458
6A:528 -A:539

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z4V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z4V)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z4V)

(-) 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:444
 aligned with HN_PIV5 | P04850 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:448
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557        
              HN_PIV5   118 INDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhh.eeeeee...............eeeeeeeee....eeeeeeee.....----.eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeeee........eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhh.ee.....eeeeeeeeeee.........eeee...........eeeeee..eeeeee.........eeeeeeeee....eeeeeeee..........hhhhh................eee..hhhhh.......eeeeeee........eeeeeee...eeeeee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z4v A 118 INDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQ----SNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                   127       137       147       157       167       177        |-   |   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557        
                                                                                              186  191                                                                                                                                                                                                                                                                                                                                                                                      

   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 1Z4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z4V)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (HN_PIV5 | P04850)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HN_PIV5 | P048501z4w 1z4x 1z4y 1z4z 1z50 3tsi 4jf7

(-) Related Entries Specified in the PDB File

1z4w 1z4x 1z4y 1z4z 1z50