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(-) Description

Title :  CRYSTAL STRUCTURE OF A CHIMERIC ALPHA1 INTEGRIN I-DOMAIN IN COMPLEX WITH THE FAB FRAGMENT OF A HUMANIZED NEUTRALIZING ANTIBODY
 
Authors :  M. Karpusas, F. Taylor, J. Ferrant, P. Weinreb, E. Garber
Date :  20 Aug 02  (Deposition) - 15 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,H,L,X,Y
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,X,Y  (1x)
Keywords :  Integrin, Cell Adhesion, Receptor, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Karpusas, J. Ferrant, P. Weinreb, A. Carmillo, F. Taylor, E. Garber
Crystal Structure Of The Alpha 1 Beta 1 Integrin I Domain In Complex With An Antibody Fab Fragment
J. Mol. Biol. V. 327 1031 2003
PubMed-ID: 12662928  |  Reference-DOI: 10.1016/S0022-2836(03)00203-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTEGRIN ALPHA 1, (RESIDUES 169-360)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentALPHA1 I-DOMAIN
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymLAMININ AND COLLAGEN RECEPTOR, VLA-1, CD49A
 
Molecule 2 - FAB FRAGMENT, HEAVY CHAIN
    ChainsH, X
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellCHO CELLS
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - FAB FRAGMENT, LIGHT CHAIN
    ChainsL, Y
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellCHO CELLS
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABHLXY
Biological Unit 1 (1x)A HL  
Biological Unit 2 (1x) B  XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:156 , SER A:158 , THR A:224 , ASP A:257 , ASP H:101BINDING SITE FOR RESIDUE MN A 400
2AC2SOFTWARESER B:156 , SER B:158 , THR B:224 , ASP X:101BINDING SITE FOR RESIDUE MN B 400

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1H:22 -H:95
2H:145 -H:201
3L:23 -L:87
4L:133 -L:193
5X:22 -X:95
6Y:23 -Y:87

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Tyr A:160 -Pro A:161
2Glu A:309 -Pro A:310
3Phe H:151 -Pro H:152
4Glu H:153 -Pro H:154
5Ser L:7 -Pro L:8
6Asn L:93 -Pro L:94
7Tyr L:139 -Pro L:140
8Tyr B:160 -Pro B:161
9Glu B:309 -Pro B:310
10Ser Y:7 -Pro Y:8
11Asn Y:93 -Pro Y:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MHP)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITA1_RAT172-355
 
  2A:148-331
B:148-331
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITA1_RAT172-355
 
  1A:148-331
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITA1_RAT172-355
 
  1-
B:148-331

(-) Exons   (0, 0)

(no "Exon" information available for 1MHP)

(-) 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:184
 aligned with ITA1_RAT | P18614 from UniProtKB/Swiss-Prot  Length:1180

    Alignment length:192
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358  
             ITA1_RAT   169 TQLDIVIVLDGSNSIYPWESVIAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAANKIGRQGGLQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNYRLKQVIQDCEDENIQRFSIAILGHYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKALGERIF 360
               SCOP domains d1mhpa_ A: Integrin alpha1-beta1                                                                                                                                                                 SCOP domains
               CATH domains 1mhpA00 A:145-336  [code=3.40.50.410, no name defined]                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhh........eeeeeee...eeeee......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.....eeeeeeee........hhhhhhhhhhhh.eeeeeeee..--------hhhhhhhhhh....hhhh.eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VWFA  PDB: A:148-331 UniProt: 172-355                                                                                                                                                   ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mhp A 145 TQLDIVIVLDGSNSIYPWESVIAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAANKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNYRLKQVIQDCEDENIQRFSIAILG--------TEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKALGERIF 336
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284  |      - |     304       314       324       334  
                                                                                                                                                                        287      296                                        

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with ITA1_RAT | P18614 from UniProtKB/Swiss-Prot  Length:1180

    Alignment length:192
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358  
             ITA1_RAT   169 TQLDIVIVLDGSNSIYPWESVIAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAANKIGRQGGLQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNYRLKQVIQDCEDENIQRFSIAILGHYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKALGERIF 360
               SCOP domains d1mhpb_ B: Integrin alpha1-beta1                                                                                                                                                                 SCOP domains
               CATH domains 1mhpB00 B:145-336  [code=3.40.50.410, no name defined]                                                                                                                                           CATH domains
           Pfam domains (1) ---VWA-1mhpB01 B:148-331                                                                                                                                                                   ----- Pfam domains (1)
           Pfam domains (2) ---VWA-1mhpB02 B:148-331                                                                                                                                                                   ----- Pfam domains (2)
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhh........eeeeeee...eeeee......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.....eeeeeeee........hhhhhhhhhhhh.eeeeeeeehhhhhhh...hhhhhhhhhh....hhhhheeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VWFA  PDB: B:148-331 UniProt: 172-355                                                                                                                                                   ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mhp B 145 TQLDIVIVLDGSNSIYPWESVIAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAANKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNYRLKQVIQDCEDENIQRFSIAILGHYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKALGERIF 336
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334  

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1mhph1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1mhph2 H:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1mhpH01 H:1-118 Immunoglobulins                                                                                       1mhpH02 H:119-218 Immunoglobulins                                                                   - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhp H   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYTMSWVRQAPGKGLEWVATISGGGHTYYLDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGFGDGGYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1mhpl1 L:2-106 Immunoglobulin light chain kappa variable domain, VL-kappa                               d1mhpl2 L:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1mhpL01 L:2-107 Immunoglobulins                                                                           1mhpL02 L:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhp L   2 IQLTQSPSSLSASVGDRVTITCSASSSVNHMFWYQQKPGKAPKPWIYLTSNLASGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCQQWSGNPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  

Chain X from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains d1mhpx_ X: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 1mhpX00 X:1-118 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.....eee........eeeeehhh.eeeeee........eeeeeeeee....eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhp X   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYTMSWVRQAPGKGLEWVATISGGGHTYYLDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGFGDGGYFDVWGQGTLVTVSS 118
                                    10        20        30        40        50        60        70        80        90       100       110        

Chain Y from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains d1mhpy_ Y: Immunoglobulin light chain kappa variable domain, VL-kappa                                     SCOP domains
               CATH domains 1mhpY00 Y:2-106 Immunoglobulins                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1mhp Y   2 IQLTQSPSSLSASVGDRVTITCSASSSVNHMFWYQQKPGKAPKPWIYLTSNLASGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCQQWSGNPWTFGQGTKVEIK 106
                                    11        21        31        41        51        61        71        81        91       101     

   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  (5, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)
1aVWA-1mhpB01B:148-331
1bVWA-1mhpB02B:148-331

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ITA1_RAT | P18614)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0098639    collagen binding involved in cell-matrix adhesion    Any collagen binding that occurs as part of cell-matrix adhesion.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    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:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0045123    cellular extravasation    The migration of a leukocyte from the blood vessels into the surrounding tissue.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:0042311    vasodilation    An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0034665    integrin alpha1-beta1 complex    An integrin complex that comprises one alpha1 subunit and one beta1 subunit.
    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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITA1_RAT | P186141ck4 2b2x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MHP)