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(-) Description

Title :  CRYSTAL STRUCTURE OF INTEGRIN ALPHA V BETA 6 HEAD
 
Authors :  X. Dong, T. A. Springer
Date :  18 Dec 15  (Deposition) - 25 Jan 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Integrin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Dong, B. Zhao, R. E. Iacob, J. Zhu, A. C. Koksal, C. Lu, J. R. Engen, T. A. Springer
Force Interacts With Macromolecular Structure In Activation Of Tgf-Beta.
Nature V. 542 55 2017
PubMed-ID: 28117447  |  Reference-DOI: 10.1038/NATURE21035

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-V
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 31-627
    Gene: ITGAV, MSK8, VNRA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VITRONECTIN RECEPTOR SUBUNIT ALPHA
 
Molecule 2 - INTEGRIN BETA-6
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 128-378
    Gene: ITGB6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 34)

Asymmetric/Biological Unit (7, 34)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA6Ligand/IonCALCIUM ION
3MAN8Ligand/IonALPHA-D-MANNOSE
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7SO41Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:284 , ASN A:286 , ASP A:288 , TYR A:290 , ASP A:292 , HOH A:2109binding site for residue CA A 2001
02AC2SOFTWAREASP A:349 , ASP A:351 , ASP A:353 , PHE A:355 , ASP A:357 , HOH A:2127binding site for residue CA A 2002
03AC3SOFTWAREASP A:414 , ASP A:416 , ASN A:418 , TYR A:420 , ASP A:422 , HOH A:2117binding site for residue CA A 2003
04AC4SOFTWAREASP A:230 , ASN A:232 , ASP A:234 , ILE A:236 , ASP A:238 , HOH A:2102binding site for residue CA A 2004
05AC5SOFTWAREARG A:510 , PRO A:520binding site for residue SO4 A 2028
06AC6SOFTWARELYS A:506 , GLY A:507 , ILE A:509 , ARG A:518 , GLU A:548 , PHE A:549 , ARG A:550 , ASP A:551binding site for residue MES A 2029
07AC7SOFTWARETYR A:516 , SER A:517 , HIS A:522 , LEU A:539binding site for residue PEG A 2030
08AC8SOFTWARESER B:127 , ASP B:130 , ASP B:131 , LYS B:338 , HOH B:2120 , HOH B:2165binding site for residue CA B 2001
09AC9SOFTWAREASP B:123 , SER B:125 , SER B:127 , GLU B:223 , ASP B:254 , HOH B:2123binding site for residue CA B 2002
10AD1SOFTWAREASP A:83 , ASP A:84 , GLN A:120 , GLN B:315binding site for residue PEG B 2004
11AD2SOFTWAREGLU A:15 , GLY A:16 , LYS A:42 , ASN A:44 , GLU A:52 , GLY A:466 , HOH A:2101binding site for Poly-Saccharide residues NAG A 2005 through NAG A 2006 bound to ASN A 44
12AD3SOFTWAREASN A:232 , ASP A:234 , ASP A:257 , LYS A:259 , ASN A:260 , HOH A:2195binding site for Poly-Saccharide residues NAG A 2007 through BMA A 2009 bound to ASN A 260
13AD4SOFTWAREALA A:213 , GLN A:214 , PHE A:217 , TYR A:254 , SER A:263 , LEU A:264 , ASN A:266 , HOH A:2159 , HOH A:2227 , GLU B:237binding site for Poly-Saccharide residues NAG A 2010 through MAN A 2015 bound to ASN A 266
14AD5SOFTWARESER A:193 , ASP A:196 , ASN A:459 , THR A:461 , CYS A:473binding site for Poly-Saccharide residues NAG A 2016 through BMA A 2018 bound to ASN A 459
15AD6SOFTWAREASP A:6 , ARG A:439 , ASN A:525 , ARG A:563 , ARG A:567 , NAG A:2027 , HOH A:2114 , HOH A:2155 , HOH A:2208binding site for Poly-Saccharide residues NAG A 2019 through MAN A 2026 bound to ASN A 525
16AD7SOFTWAREPHE A:559 , PRO A:584 , ASN A:586 , MAN A:2026binding site for Mono-Saccharide NAG A 2027 bound to ASN A 586
17AD8SOFTWAREASN B:243binding site for Mono-Saccharide NAG B 2003 bound to ASN B 243

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:67
2A:108 -A:128
3A:142 -A:155
4A:401 -B:270
5A:462 -A:473
6A:479 -A:536
7B:180 -B:187
8B:235 -B:276

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:451 -Pro A:452
2Ser B:166 -Pro B:167
3Ile B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FFG)

(-) 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:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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....................eeee....eeeeee.hhhhhh.eeeeeehhhhhhh.............ee....hhhhh.......eeee........eeeeee.hhhhhh.eeeee......eeeeee...........eeee........eeeeee...eee.....eee..eeeeeee.....eeeeeee...........eeeee........eeeeee...hhhhh.eeeeeeee..ee.....eeee...............eeeeee........eeeeeehhh.eeeee....eeeeeeeeeee..eee................eeeeeeeeeee.......eeeeeeeee............eee......eeeeeeeee.....eeeeeeeee.hhhhh......eeeeeeeee.............ee......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ffg A   1 FNLDVDSPAEYSGPEGSYFGFAVDFFVPSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHIL 594
                                    10        20       |33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593 
                                                      28|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                       32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhhhhhhhhhh.hhhhhhhhhhhhhh..eeeeeeee...........hhhhhhh..............eeeeeeee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhh..........................hhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ffg B 113 DYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVEL 360
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
   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 5FFG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (76, 89)

Asymmetric/Biological Unit(hide GO term definitions)

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  ITB6_HUMAN | P18564
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 Related Entries

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

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

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