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(-) Description

Title :  STRUCTURE OF THE PARAINFLUENZA VIRUS 5 (PIV5) HEMAGGLUTININ-NEURAMINIDASE (HN) ECTODOMAIN
 
Authors :  B. D. Welch, P. Yuan, S. Bose, C. A. Kors, R. A. Lamb, T. S. Jardetzky
Date :  27 Feb 13  (Deposition) - 04 Sep 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Paramyxovirus, Piv5, Attachment Protein, Hn, Receptor Binding Protein, Ectodomain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Welch, P. Yuan, S. Bose, C. A. Kors, R. A. Lamb, T. S. Jardetzky
Structure Of The Parainfluenza Virus 5 (Piv5) Hemagglutinin-Neuraminidase (Hn) Ectodomain.
Plos Pathog. V. 9 03534 2013
PubMed-ID: 23950713  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003534

(-) Compounds

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
    Chains: D, A, B, C
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PBACGUS-11
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: ECTODOMAIN
    Gene: HN
    Organism Common: SV5
    Organism Scientific: SIMIAN VIRUS 5
    Organism Taxid: 11208
    Strain: W3

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO44Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP D:250 , SER D:253 , ALA D:255 , ALA D:285 , HOH D:821BINDING SITE FOR RESIDUE CA D 601
02AC2SOFTWAREPRO D:233 , TYR D:265 , GLN D:369 , MAN D:603 , NAG D:604 , HOH D:854BINDING SITE FOR RESIDUE NAG D 602
03AC3SOFTWARENAG D:602BINDING SITE FOR RESIDUE MAN D 603
04AC4SOFTWAREGLY D:234 , ASN D:267 , THR D:269 , GLN D:369 , NAG D:602BINDING SITE FOR RESIDUE NAG D 604
05AC5SOFTWAREGLN D:507 , NAG D:606 , MAN D:607 , HOH D:881BINDING SITE FOR RESIDUE NAG D 605
06AC6SOFTWAREASN D:504 , ASN D:505 , THR D:506 , GLN D:507 , ILE D:509 , NAG D:605BINDING SITE FOR RESIDUE NAG D 606
07AC7SOFTWARENAG D:605 , HOH D:913BINDING SITE FOR RESIDUE MAN D 607
08AC8SOFTWAREARG D:405 , ARG D:495BINDING SITE FOR RESIDUE SO4 D 608
09AC9SOFTWAREASN D:139BINDING SITE FOR RESIDUE NAG D 609
10BC1SOFTWAREASP A:250 , SER A:253 , ALA A:255 , ALA A:285 , HOH A:723BINDING SITE FOR RESIDUE CA A 601
11BC2SOFTWAREASN A:139BINDING SITE FOR RESIDUE NAG A 602
12BC3SOFTWAREASN A:267 , THR A:269 , GLN A:369 , NAG A:604 , HOH A:768 , GLN B:109BINDING SITE FOR RESIDUE NAG A 603
13BC4SOFTWAREGLN A:369 , NAG A:603BINDING SITE FOR RESIDUE NAG A 604
14BC5SOFTWAREGLU A:481 , ASN A:504 , THR A:506 , GLN A:507 , ILE A:509 , NAG A:606 , HOH A:820BINDING SITE FOR RESIDUE NAG A 605
15BC6SOFTWAREGLN A:507 , NAG A:605BINDING SITE FOR RESIDUE NAG A 606
16BC7SOFTWAREARG A:405 , ARG A:495 , TYR A:523 , HOH A:848 , HOH A:857BINDING SITE FOR RESIDUE SO4 A 607
17BC8SOFTWARELEU A:107 , ASN A:110BINDING SITE FOR RESIDUE NAG A 608
18BC9SOFTWAREASP B:250 , SER B:253 , ALA B:255 , ALA B:285BINDING SITE FOR RESIDUE CA B 601
19CC1SOFTWAREARG B:163 , ARG B:405 , ARG B:495 , TYR B:523BINDING SITE FOR RESIDUE SO4 B 602
20CC2SOFTWAREGLU A:108 , GLN A:109 , ASN B:267 , THR B:269 , GLN B:369 , NAG B:604BINDING SITE FOR RESIDUE NAG B 603
21CC3SOFTWARETYR B:265 , GLN B:369 , NAG B:603 , HOH B:790BINDING SITE FOR RESIDUE NAG B 604
22CC4SOFTWAREGLU B:481 , ASN B:504 , THR B:506 , GLN B:507 , HOH B:715BINDING SITE FOR RESIDUE NAG B 605
23CC5SOFTWAREASP C:250 , SER C:253 , ALA C:255 , ALA C:285 , HOH C:751BINDING SITE FOR RESIDUE CA C 601
24CC6SOFTWAREARG C:163 , ARG C:405 , ARG C:495 , TYR C:523BINDING SITE FOR RESIDUE SO4 C 602
25CC7SOFTWAREASN C:139 , HOH C:824BINDING SITE FOR RESIDUE NAG C 603
26CC8SOFTWAREASN C:267 , THR C:269 , GLN C:369BINDING SITE FOR RESIDUE NAG C 604
27CC9SOFTWAREGLU C:481 , ASN C:504 , THR C:506 , GLN C:507 , ILE C:509 , NAG C:606BINDING SITE FOR RESIDUE NAG C 605
28DC1SOFTWAREGLN C:507 , NAG C:605BINDING SITE FOR RESIDUE NAG C 606

(-) SS Bonds  (29, 29)

Asymmetric/Biological Unit
No.Residues
1A:111 -B:111
2A:161 -A:185
3A:175 -A:236
4A:227 -A:240
5A:333 -A:454
6A:365 -A:375
7A:448 -A:458
8A:528 -A:539
9B:161 -B:185
10B:175 -B:236
11B:227 -B:240
12B:333 -B:454
13B:365 -B:375
14B:448 -B:458
15B:528 -B:539
16C:161 -C:185
17C:175 -C:236
18C:227 -C:240
19C:333 -C:454
20C:365 -C:375
21C:448 -C:458
22C:528 -C:539
23D:161 -D:185
24D:175 -D:236
25D:227 -D:240
26D:333 -D:454
27D:365 -D:375
28D:448 -D:458
29D:528 -D:539

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JF7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JF7)

(-) 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:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee.....................hhhh.eeeeee...............eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh.....eeeeeee....eeeeee........eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhh.ee.....eeeeeeeeeee.........eeee...........eeeeee..eeeeee.........eeeeeeeeee..eeeeeeeee...............................eee..hhhhh........eeeeee........eeeeee....eeeeee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jf7 A  61 ITDLLNNILSVANQIIYNSAVALPLQLDTLESTLLTAIKSLQLEQNCSWSAALINDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                    70        80        90       100 ||    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       514       524       534       544       554       564 
                                                                   102|                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                    107                                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhh..hhhhhh.........hhhh.eeeeeee..............eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh.....eeeeeee....eeeee.........eeeeee.....eee..eeeeeeeeee...hhhhhhhh........hhhhh..hhhhhhhhhhhh.ee.....eeeeeeeeeee.........eeee...........eeeeee..eeeeee.........eeeeeeeeee..eeeeeeeee..........hhhhh................eee..hhhhh........eeeeee........eeeeee....eeeeee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jf7 B  65 LNNILSVANQIIYNSAVALPLQLDTLESTLLTAIKSLQTSDKLEQNCSWSAALINDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                    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       514       524       534       544       554       564 


Chain C from PDB  Type:PROTEIN  Length:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhh.......hhhhhh.eeeeeee..............eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh.....eeeeeee....eeeee.........eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhh..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
                 4jf7 C  64 LLNNILSVANQIIYNSAVALPLQLDTLESTLLTAIKSLCSWSAALINDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                    73        83        93       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       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562   
                                                               101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                111                                                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhh.eeeeee...............eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeeee........eeeeee.....eee..eeeeeeeeee...hhhhhhhh.......hhhhhh..hhhhhhhhhhhh.ee.....eeeeeeeeeee.........eeee...........eeeeee..eeeeee.........eeeeeeeeee..eeeeeeeee..........hhhhh................eee...............eeeeee........eeeeee....eeeeee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jf7 D  62 TDLLNNILSVANQIIYNSAVALPLQLDTLESTLLTAIKSLSAALINDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                    71        81        91       101|      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       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563  
                                                                 101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                  114
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  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 4JF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JF7)

(-) Gene Ontology  (18, 18)

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        HN_PIV5 | P04850: 1z4v 1z4w 1z4x 1z4y 1z4z 1z50 3tsi

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