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(-) Description

Title :  STRUCTURE OF THE CALX-BETA DOMAIN OF INTEGRIN BETA4 CRYSTALLIZED IN THE PRESENCE OF CALCIUM
 
Authors :  N. Alonso-Garcia, A. Ingles-Prieto, J. M. De Pereda
Date :  23 Apr 09  (Deposition) - 23 Jun 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immunoglobulin Fold, Integrin, Cell Adhesion, Epidermolysis Bullosa, Glycoprotein, Membrane, Receptor, Transmembrane, Alternative Splicing, Disease Mutation, Disulfide Bond, Phosphoprotein, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Alonso-Garcia, A. Ingles-Prieto, A. Sonnenberg, J. M. De Pereda
Structure Of The Calx-Beta Domain Of The Integrin Beta4 Subunit: Insights Into Function And Cation-Independent Stability
Acta Crystallogr. , Sect. D V. 65 858 2009
PubMed-ID: 19622870  |  Reference-DOI: 10.1107/S0907444909018745
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTEGRIN BETA-4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCALX-BETA DOMAIN, RESIDUES 989-1107
    GeneITGB4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGP150

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3H6A)

(-) Sites  (0, 0)

(no "Site" information available for 3H6A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H6A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:1094 -Pro A:1095
2Gln B:1094 -Pro B:1095

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H6A)

(-) Exons   (4, 7)

Asymmetric Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002001811ENSE00001241194chr17:73717516-73717692177ITB4_HUMAN-00--
1.2aENST000002001812aENSE00001324771chr17:73720774-7372086289ITB4_HUMAN1-27270--
1.3ENST000002001813ENSE00001124485chr17:73723275-7372335783ITB4_HUMAN27-54280--
1.4ENST000002001814ENSE00000949747chr17:73723485-73723586102ITB4_HUMAN55-88340--
1.5ENST000002001815ENSE00001124471chr17:73723732-73723936205ITB4_HUMAN89-157690--
1.6ENST000002001816ENSE00001124465chr17:73724458-7372455497ITB4_HUMAN157-189330--
1.7ENST000002001817ENSE00001124457chr17:73725346-73725517172ITB4_HUMAN189-246580--
1.8ENST000002001818ENSE00001124449chr17:73726322-73726585264ITB4_HUMAN247-334880--
1.9ENST000002001819ENSE00001124443chr17:73726956-7372704590ITB4_HUMAN335-364300--
1.10ENST0000020018110ENSE00001124439chr17:73727327-73727449123ITB4_HUMAN365-405410--
1.11ENST0000020018111ENSE00001124435chr17:73727893-73728054162ITB4_HUMAN406-459540--
1.12ENST0000020018112ENSE00001124428chr17:73728244-7372832077ITB4_HUMAN460-485260--
1.13ENST0000020018113ENSE00001124422chr17:73729571-73729773203ITB4_HUMAN485-553690--
1.14ENST0000020018114ENSE00001124416chr17:73732132-73732235104ITB4_HUMAN553-587350--
1.15ENST0000020018115ENSE00001124412chr17:73732369-7373246799ITB4_HUMAN588-620330--
1.16ENST0000020018116ENSE00001124406chr17:73732646-73732775130ITB4_HUMAN621-664440--
1.17ENST0000020018117ENSE00001124401chr17:73733403-73733525123ITB4_HUMAN664-705420--
1.18ENST0000020018118ENSE00001124394chr17:73733619-73733725107ITB4_HUMAN705-740360--
1.19ENST0000020018119ENSE00000949763chr17:73735753-7373578634ITB4_HUMAN741-752120--
1.20ENST0000020018120ENSE00000949766chr17:73735961-73736152192ITB4_HUMAN752-816650--
1.21aENST0000020018121aENSE00000949770chr17:73736439-73736542104ITB4_HUMAN816-850350--
1.22ENST0000020018122ENSE00001687345chr17:73736874-7373693259ITB4_HUMAN851-870200--
1.23ENST0000020018123ENSE00001619429chr17:73737063-7373708624ITB4_HUMAN870-87890--
1.24ENST0000020018124ENSE00001805264chr17:73738422-73738570149ITB4_HUMAN878-928510--
1.25ENST0000020018125ENSE00001680833chr17:73738663-73738842180ITB4_HUMAN928-988612A:988-988
B:988-988
1
1
1.26ENST0000020018126ENSE00001768237chr17:73739794-73739942149ITB4_HUMAN988-1037502A:988-1037
B:988-1037
50
50
1.27ENST0000020018127ENSE00001689069chr17:73744922-73745126205ITB4_HUMAN1038-1106692A:1038-1105 (gaps)
B:1038-1106 (gaps)
68
69
1.28ENST0000020018128ENSE00001774407chr17:73746192-73746349158ITB4_HUMAN1106-1158531-
B:1106-1107
-
2
1.29ENST0000020018129ENSE00001767853chr17:73746761-73746941181ITB4_HUMAN1159-1219610--
1.30ENST0000020018130ENSE00001697152chr17:73747055-73747192138ITB4_HUMAN1219-1265470--
1.31ENST0000020018131ENSE00001652055chr17:73748255-73748437183ITB4_HUMAN1265-1326620--
1.32ENST0000020018132ENSE00001699238chr17:73748527-73748658132ITB4_HUMAN1326-1370450--
1.33ENST0000020018133ENSE00001194868chr17:73749846-73750055210ITB4_HUMAN1370-1440710--
1.34ENST0000020018134ENSE00001639205chr17:73750657-73750896240ITB4_HUMAN1440-1520810--
1.36ENST0000020018136ENSE00001653111chr17:73751782-73751931150ITB4_HUMAN1520-1570510--
1.37ENST0000020018137ENSE00001797424chr17:73752510-73752698189ITB4_HUMAN1570-1633640--
1.38bENST0000020018138bENSE00001690108chr17:73752785-73752940156ITB4_HUMAN1633-1685530--
1.39ENST0000020018139ENSE00001630802chr17:73753024-73753188165ITB4_HUMAN1685-1740560--
1.40ENST0000020018140ENSE00001616309chr17:73753281-73753391111ITB4_HUMAN1740-1777380--
1.41ENST0000020018141ENSE00001631008chr17:73753497-73753898402ITB4_HUMAN1777-1822460--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:109
 aligned with ITB4_HUMAN | P16144 from UniProtKB/Swiss-Prot  Length:1822

    Alignment length:118
                                   997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097        
          ITB4_HUMAN    988 ARDVVSFEQPEFSVSRGDQVARIPVIRRVLDGGKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLELQEVDSLLRGRQVRRFHVQLSNPKFGAHLGQPHSTTIIIRDP 1105
               SCOP domains d3h6aa_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeee....eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee....---------..eeeeeeeeeeee...ee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-------------------------------------------------Exon 1.27  PDB: A:1038-1105 (gaps) UniProt: 1038-1106 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) Exon 1.26  PDB: A:988-1037 UniProt: 988-1037      -------------------------------------------------------------------- Transcript 1 (2)
                3h6a A  988 MRDVVSFEQPEFSVSRGDQVARIPVIRRVLDGGKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLEL---------RQVRRFHVQLSNPKFGAHLGQPHSTTIIIRDP 1105
                                   997      1007      1017      1027      1037      1047      1057      |  -      1077      1087      1097        
                                                                                                     1064      1074                               

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with ITB4_HUMAN | P16144 from UniProtKB/Swiss-Prot  Length:1822

    Alignment length:120
                                   997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107
          ITB4_HUMAN    988 ARDVVSFEQPEFSVSRGDQVARIPVIRRVLDGGKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLELQEVDSLLRGRQVRRFHVQLSNPKFGAHLGQPHSTTIIIRDPDE 1107
               SCOP domains d3h6ab_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeee....eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee....-----......eeeeeeeeeeee...ee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1-------------------------------------------------Exon 1.27  PDB: B:1038-1106 (gaps) UniProt: 1038-1106                - Transcript 1 (1)
           Transcript 1 (2) Exon 1.26  PDB: B:988-1037 UniProt: 988-1037      --------------------------------------------------------------------1. Transcript 1 (2)
                3h6a B  988 MRDVVSFEQPEFSVSRGDQVARIPVIRRVLDGGKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLEL-----LLRGRQVRRFHVQLSNPKFGAHLGQPHSTTIIIRDPDE 1107
                                   997      1007      1017      1027      1037      1047      1057      |  -  |   1077      1087      1097      1107
                                                                                                     1064  1070                                     

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H6A)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ITB4_HUMAN | P16144)
molecular function
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    GO:0031994    insulin-like growth factor I binding    Interacting selectively and non-covalently with insulin-like growth factor I.
    GO:0038132    neuregulin binding    Interacting selectively and non-covalently with a neuregulin, a member of the EGF family of growth factors.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0097186    amelogenesis    The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007154    cell communication    Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0048870    cell motility    Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0031581    hemidesmosome assembly    Assembly of hemidesmosomes, integrin-containing protein complexes that bind to laminin in the basal lamina. Hemidesmosomes form the contact between the basal surface of epithelial cells and the underlying basal lamina.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048333    mesodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
    GO:0035878    nail development    The process whose specific outcome is the progression of a nail over time, from its formation to the mature structure. A nail is a horn-like envelope covering the outer end of a finger or toe, and consists of the nail plate, the nail matrix and the nail bed below it, and the grooves surrounding it.
    GO:0072001    renal system development    The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0030056    hemidesmosome    A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0008305    integrin complex    A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITB4_HUMAN | P161441qg3 2yrz 3f7p 3f7q 3f7r 3fq4 3fso 4q58 4wtw 4wtx

(-) Related Entries Specified in the PDB File

3fq4 STRUCTURE OF THE SAME REGION OF BETA4 INTEGRIN
3fso STRUCTURE OF THE SAME REGION OF BETA4 INTEGRIN