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(-) Description

Title :  LOCALISED RECONSTRUCTION OF ALPHA V BETA 6 BOUND TO FOOT AND MOUTH DISEASE VIRUS O PANASIA - POSE A
 
Authors :  A. Kotecha, D. Stuart
Date :  10 Mar 17  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,1,2,3,4
Keywords :  Foot And Mouth Disease Virus, Fmdv, Virus, Opanasia, Virus-Receptor, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kotecha, Q. Wang, X. Dong, S. L. Ilca, M. Ondiviela, R. Zihe, J. Seago B. Charleston, E. E. Fry, N. G. A. Abrescia, T. A. Springer, J. T. Huiskonen, D. I. Stuart
Rules Of Engagement Between Alpha V Beta 6 Integrin And Foot-And-Mouth Disease Virus.
Nat Commun V. 8 15408 2017
PubMed-ID: 28534487  |  Reference-DOI: 10.1038/NCOMMS15408

(-) Compounds

Molecule 1 - O PANASIA VP1
    Chains: 1
    Engineered: YES
    Expression System: CRICETINAE GEN. SP.
    Expression System Cell Line: BHK 21
    Expression System Taxid: 36483
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE O
    Organism Taxid: 12118
 
Molecule 2 - O PANASIA VP2
    Chains: 2
    Engineered: YES
    Expression System: CRICETINAE GEN. SP.
    Expression System Taxid: 36483
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE O
    Organism Taxid: 12118
 
Molecule 3 - O PANASIA VP3
    Chains: 3
    Engineered: YES
    Expression System: CRICETINAE GEN. SP.
    Expression System Taxid: 36483
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE O
    Organism Taxid: 12118
 
Molecule 4 - O PANASIA VP4
    Chains: 4
    Engineered: YES
    Expression System: CRICETINAE GEN. SP.
    Expression System Taxid: 36483
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE O
    Organism Taxid: 12118
 
Molecule 5 - INTEGRIN ALPHA-V
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: ITGAV, MSK8, VNRA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VITRONECTIN RECEPTOR SUBUNIT ALPHA
 
Molecule 6 - INTEGRIN BETA-6
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: ITGB6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : AB1234

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric/Biological Unit (3, 26)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MAN11Ligand/IonALPHA-D-MANNOSE
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:494 , SER A:522 , ASN A:524binding site for residue NAG A 613
02AC2SOFTWAREASP A:415 , ASN A:417 , TYR A:419 , ASP A:421 , ALA A:437binding site for residue CA A 618
03AC3SOFTWAREASP A:349 , ASP A:351 , ASP A:353 , PHE A:355 , ASP A:357binding site for residue CA A 619
04AC4SOFTWAREASP A:230 , ASN A:232 , ASP A:234 , ILE A:236 , ASP A:238binding site for residue CA A 620
05AC5SOFTWAREASP A:284 , ASN A:286 , ASP A:288 , TYR A:290 , ASP A:292binding site for residue CA A 621
06AC6SOFTWARETYR A:450 , ASN A:455 , ASN A:458 , THR A:460 , CYS A:472 , ASN A:474binding site for Poly-Saccharide residues NAG A 609 through MAN A 612 bound to ASN A 458
07AC7SOFTWAREASN B:77 , SER B:79 , ASP B:80binding site for Mono-Saccharide NAG B 501 bound to ASN B 77
08AC8SOFTWAREASN A:232 , SER A:262binding site for Poly-Saccharide residues NAG A 601 through MAN A 603
09AC9SOFTWAREASN A:232 , NAG A:601binding site for Poly-Saccharide residues NAG A 604 through MAN A 606
10AD1SOFTWAREPHE A:558 , PRO A:583 , ALA A:584 , ASN A:585binding site for Poly-Saccharide residues NAG A 614 through MAN A 617

(-) SS Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:67
2A:108 -A:128
3A:142 -A:155
4A:400 -B:267
5A:461 -A:472
6A:478 -A:535
7B:6 -B:24
8B:14 -B:434
9B:17 -B:39
10B:27 -B:50
11B:177 -B:184
12B:232 -B:273
13B:374 -B:386
14B:406 -B:432
15B:436 -B:456
16B:447 -B:459
17B:461 -B:470

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala 1:110 -Pro 1:111
2Leu 2:83 -Pro 2:84
3Tyr A:450 -Pro A:451
4Ala B:85 -Pro B:86
5Ser B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NEM)

(-) Exons   (0, 0)

(no "Exon" information available for 5NEM)

(-) 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 1 from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..........hhhhhh...........hhhhhh..eeee.....eee.hhhhh...hhhhhhhh.eeeeeeeeeeeeeee..eeee.....hhhhhh....ee......eeeee........ee....................hhhhhh.............eee..eeeeeeeeeeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5nem 1   1 TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHTLVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPETALDNTTNPTAYHKAPLTRLALPYTAPHRVLATAYNGNCKYGESHTTNVRGDLQVLAQKVARTLPTSFNYGAIKATRVTELLYRMKRAETYCPRPLLAIHPSEARHKQKIVAPVK 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain 2 from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeee.....eee.................eee.hhhh..eeeeeeee..........eeee.......hhhhh..eeeeeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhh.eeee......eeeeee................eeeeeeeeeeeee.......eeeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nem 2   5 EETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATTEDFVSGPNTSGLETRVVQAERFFKTHLFDWVTSDSFGRCHLLELPTDHKGVYGSLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVAMVPELCSINKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLVVMVVAPLTVNTEGAPQIKVYANIAPTNVHVAGEFPSKE 218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    


Chain 3 from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee..................hhhhhhhhh.ee........ee........eeeeee.....hhhhhhhhhhhh..eeeee..eeeeeee......eeeeeeeee........hhhhhh..eeeeee.....eeeeee........ee.............eeeeeeeeee......eeeeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nem 3   1 GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLRFEGDVPYVTTKTDSDRILAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKARYMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYAYTASDTAETTNVQGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain 4 from PDB  Type:PROTEIN  Length:47
                                                                               
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.........hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 5nem 4  15 SGNTGSIINNYYMQQYQNSMDTQLGDNDWFSKLASSAFSGLFGALLA  85
                                    24        34     || 68        78       
                                                    40|                    
                                                     65                    


Chain A from PDB  Type:PROTEIN  Length:589
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..........eeee......eeeeee..............eeeeee......eeee........eee..ee.ee.........eeee..eeeeee...ee............eeeeee..eeeee.....................eee....eeeeee.hhhhhh.eeeeeehhhhhhh............eee....hhhhh.......eeee........eeeeee.hhhhhh.eeeee........eee...........eeee........eeeeee...eee.....eee..eeeeeee.....eeeeeee...........eeeee........eeeeee...hhhhh.eeeeee...........eeee..............eeeeee........eeeeeehhh.eeeee....eeee..eeeee..ee.................eeeeeeee.ee.......eeeeeeeeee.........eee......eeeeeeeee.....eeeeeeeee.hhhhh......eeeeeeeeehhhhhh.......ee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nem A   1 FNLDVDSPAEYSGPEGSYFGFAVDFFVPSSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL 594
                                    10        20        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262||     273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503|      515       525       535       545       555       565       575       585         
                                                       29|                                                                                                                                                                                                                                    263|                                                                                                                                                                                                                                           503|                                                                                        
                                                        32                                                                                                                                                                                                                                     265                                                                                                                                                                                                                                            506                                                                                        


Chain B from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh....eee..ee.......ee....eeeeee..........hhhhh..ee..eeeeee.....eeeeeeee......eeeeeeee......hhhhh...hhhhhhhhhhh....eeeeeeee...........hhhhhhh..............eeeeeeee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhh................hhhhhh....hhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeeee......eeeeeee.....eee...ee.......eeeeeeeee........eeeeeee......eeeeeee...hhhhh............eeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nem B   5 GCALGGTCEDCLLIGPQCAWCARCDTPCQLNFIENPVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLGDALELLVSPECNCDCQKVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCE 471
                                 || 16        26 ||   ||52        62        72        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       402       412       422       432     ||443       453       463        
                                10|             28|  42|                                                                                                                                                                                                                                                                                                                                                                                                 438|                               
                                 13              38   50                                                                                                                                                                                                                                                                                                                                                                                                  440
   Legend:   → Mismatch (orange background)
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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 5NEM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NEM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NEM)

(-) Gene Ontology  (109, 129)

Asymmetric/Biological Unit(hide GO term definitions)

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  5nem
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 Related Entries

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

UniProtKB/Swiss-Prot
        A6Y878_9PICO | A6Y878: 5ner
        ITAV_HUMAN | P06756: 1jv2 1l5g 1m1x 1u8c 3ije 4g1e 4g1m 4mmx 4mmy 4mmz 4o02 4um8 4um9 5ffg 5ffo 5ner 5net 5neu
        ITB6_HUMAN | P18564: 1lh9 4um8 4um9 5ffg 5ffo 5ner 5net 5neu
        J3T9N5_9PICO | J3T9N5: 5ne4 5ned 5ner

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5NEM)