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(-) Description

Title :  LOCALISED RECONSTRUCTION OF INTEGRIN ALPHA V BETA 6 BOUND TO FOOT AND MOUTH DISEASE VIRUS O1 MANISA - POSE B
 
Authors :  A. Kotecha, D. Stuart
Date :  11 Mar 17  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.10
Chains :  Asym. Unit :  A,B,1,2,3,4
Biol. Unit 1:  A,B,1,2,3,4  (60x)
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 - O1 MANISA VP1
    Chains1
    EngineeredYES
    Expression SystemCRICETINAE GEN. SP.
    Expression System Taxid36483
    Organism ScientificFOOT-AND-MOUTH DISEASE VIRUS
    Organism Taxid12110
 
Molecule 2 - O1 MANISA VP2
    Chains2
    EngineeredYES
    Expression SystemCRICETINAE GEN. SP.
    Expression System Taxid36483
    MutationYES
    Organism ScientificFOOT-AND-MOUTH DISEASE VIRUS
    Organism Taxid12110
 
Molecule 3 - CAPSID PROTEIN
    Chains3
    EngineeredYES
    Expression SystemCRICETINAE GEN. SP.
    Expression System Taxid36483
    Organism ScientificFOOT-AND-MOUTH DISEASE VIRUS
    Organism Taxid12110
 
Molecule 4 - O1 MANISA VP4
    Chains4
    EngineeredYES
    Expression SystemCRICETINAE GEN. SP.
    Expression System Taxid36483
    Organism ScientificFOOT-AND-MOUTH DISEASE VIRUS
    Organism Taxid12110
 
Molecule 5 - INTEGRIN ALPHA-V
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293S
    Expression System CommonHUMAN
    Expression System Taxid9606
    GeneITGAV, MSK8, VNRA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVITRONECTIN RECEPTOR SUBUNIT ALPHA
 
Molecule 6 - INTEGRIN BETA-6
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293S
    Expression System CommonHUMAN
    Expression System Taxid9606
    GeneITGB6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit AB1234
Biological Unit 1 (60x)AB1234

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP 1:147 , ASP B:102 , SER B:104 , GLU B:202 , ALA B:234binding site for residue MG 1 2001
2AC2SOFTWAREGLU B:141 , ASN B:197 , ASP B:199 , PRO B:201 , GLU B:202binding site for residue CA B 601
3AC3SOFTWAREASP B:109 , ASP B:110 , LYS B:317 , ASP B:318binding site for residue CA B 602

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:59 -A:67
2A:108 -A:128
3A:142 -A:155
4A:400 -B:249
5A:461 -A:472
6A:478 -A:535
7B:6 -B:22
8B:12 -B:503
9B:15 -B:28
10B:25 -B:32
11B:159 -B:166
12B:214 -B:255
13B:443 -B:455
14B:475 -B:501
15B:505 -B:524
16B:515 -B:527
17B:529 -B:538

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ala 1:110 -Pro 1:111
2Asn 1:131 -Gly 1:132
3Tyr 1:136 -Gly 1:137
4Gly 1:137 -Asp 1:138
5Ala 1:142 -Asn 1:143
6Val 1:144 -Arg 1:145
7Leu 2:83 -Pro 2:84
8Tyr A:450 -Pro A:451
9Ala B:67 -Pro B:68
10Ser B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NEU)

(-) 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 1 from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........hhhhhh....................eee.....eee.hhhhh...hhhhhh...eeeeeeeeeeeeeee..eeee....hhhhhh.....ee......eeee.........ee.......................................eee..eeeeeeeeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5neu 1   1 TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHTLVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYTAPHRVLATVYNGNSKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRMKRAETYCPRPLLAIHPDQARHKQKIVAP 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        

Chain 2 from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee......eee.................eee.hhhh..eeeeeeee.........eeeee.....hhhhhhhh.eeeeeeeeeeeeee........eeeeeeee.......hhhhhhhhh.eeee......eeeeee................eeeeeeeee...........eeeeeee.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5neu 2  12 DRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAERFFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLVVMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE 218
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       

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........eee.......eeeeee...........hhhhhh..eeeee..eeeeeee......eeeeeeeee..........hhhhhh..eeee.....eeeeee........ee.............eeeeeeeeee.....eeeeeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5neu 3   1 GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGDVPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKARYMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTYTASDVAETTNVQGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ 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:45
                                                                             
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 5neu 4  15 SGNTGSIINNYYMQQYQNSMDTQLGDWFSKLASSAFSGLFGALLA  85
                                    24        34    ||  70        80     
                                                   39|                   
                                                    66                   

Chain A from PDB  Type:PROTEIN  Length:590
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..........eeee......eeeeee..............eeeeee.....eeeee................ee........eeeee..eeeeee...ee........ee..eeeeee..eeeee......................ee....eee....hhhhhh....eeehhhhhhhh..............................ee...........eeeee........eeeee......eeee...............ee........eeee.....ee.......ee..eeeeee.......eeeeee..........eeeeee........eeeeee...hhhhh.eeeee.............................................eeeee....eeeee....eeeee..eeee.....................eeeeeeeeeee........eeeeeeee..........eee.......eeeeeee......eeeeeeeee..............eeeeeee.............ee......eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5neu A   1 FNLDVDSPAEYSGPEGSYFGFAVDFFVPSSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL 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       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502||     514       524       534       544       554       564       574       584       594
                                                       29|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    503|                                                                                        
                                                        32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     506                                                                                        

Chain B from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...ee...ee.............eeee.......................eeeee.....eee..ee........eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhh..eee...ee...........hhhhhh.........................hhhhhhhhhhh...........hhhhhhhh.............eeeeeee......hhhhhhhhh................hhhhhh....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..ee.........hhhhhhhhhhhhh.....eeee...........ee.....ee...............ee..eee........eeeeeee.......eeee......................eeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5neu B   5 GCALGGTCEDCLLIGPQCAWCARCDTPCQLNFIENPVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLGDALELLVSPECNCDCQKVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCE 539
                                    14        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 ||    431       441       451       461       471       481       491       501       511       521       531        
                                                                                                                                                                                                                                                                                                                                                                     336|                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                      424                                                                                                                   

   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 5NEU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 161)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Ala 1:142 - Asn 1:143   [ RasMol ]  
    Ala B:67 - Pro B:68   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        E1ACS1_9PICO | E1ACS15nej 5net
        ITAV_HUMAN | P067561jv2 1l5g 1m1x 1u8c 3ije 4g1e 4g1m 4mmx 4mmy 4mmz 4o02 4um8 4um9 5ffg 5ffo 5nem 5ner 5net
        ITB6_HUMAN | P185641lh9 4um8 4um9 5ffg 5ffo 5nem 5ner 5net
        Q6PMW3_9PICO | Q6PMW35nej 5net
UniProtKB/TrEMBL
        Q6PMW3_9PICO | Q6PMW35ac9 5ddj

(-) Related Entries Specified in the PDB File

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