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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN BETA-2-SYNTROPHIN PDZ DOMAIN
 
Authors :  Z. Sun, A. K. Roos, A. C. W. Pike, E. S. Pilka, C. Cooper, J. M. Elkins, J. Mu C. H. Arrowsmith, D. Doyle, A. Edwards, F. Von Delft, C. Bountra, U. Op
Date :  31 Mar 08  (Deposition) - 22 Apr 08  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B  (1x)
Biol. Unit 6:  C,D  (1x)
Keywords :  Protein Binding, Microtubule, Cytoskeleton, Actin-Binding, Sntb2, Membrane, Calmodulin-Binding, Cytoplasmic Vesicle, Adapter Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Sun, A. K. Roos, A. C. W. Pike, E. S. Pilka, C. Cooper, J. M. Elkins, J. Murray, C. H. Arrowsmith, D. Doyle, A. Edwards, F. Von Delft, C. Bountra, U. Oppermann
Crystal Structure Of The Human Beta-2-Syntrophin Pdz Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-2-SYNTROPHIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentPDZ DOMAIN, RESIDUES 112-200
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1 BASIC COMPONENT 2, SYNTROPHIN-3, SNT3, SYNTROPHIN-LIKE, SNTL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)AB  
Biological Unit 6 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:115 , SER C:165 , ASN C:167 , GLY C:168 , LEU C:191 , HOH C:2022BINDING SITE FOR RESIDUE EDO C1205
2AC2SOFTWAREGLN A:153 , SER A:154BINDING SITE FOR RESIDUE EDO A1205
3AC3SOFTWAREARG A:115 , SER A:165 , ASN A:167 , GLY A:168 , LEU A:191 , GLU A:193BINDING SITE FOR RESIDUE EDO A1206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VRF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VRF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VRF)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  4A:115-198
B:115-198
C:115-198
D:115-198
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  1A:115-198
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  1-
B:115-198
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  1-
-
C:115-198
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  1-
-
-
D:115-198
Biological Unit 5 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  2A:115-198
B:115-198
-
-
Biological Unit 6 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SNTB2_HUMAN115-198
 
 
 
  2-
-
C:115-198
D:115-198

(-) Exons   (0, 0)

(no "Exon" information available for 2VRF)

(-) 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:95
 aligned with SNTB2_HUMAN | Q13425 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:101
                                   119       129       139       149       159       169       179       189       199       209 
          SNTB2_HUMAN   110 SPPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVTPYIKKPSLV 210
               SCOP domains d2vrfa_ A: automated matches                                                                          SCOP domains
               CATH domains 2vrfA00 A:-1-204  [code=2.30.42.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.....------ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:115-198 UniProt: 115-198                                                ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2vrf A  -1 SMPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVN------TVV 204
                             ||    119       129       139       149       159       169       179       189       199 |     203 
                             0|                                                                                      201    202  
                            112                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with SNTB2_HUMAN | Q13425 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:101
                                   119       129       139       149       159       169       179       189       199       209 
          SNTB2_HUMAN   110 SPPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVTPYIKKPSLV 210
               SCOP domains d2vrfb_ B: automated matches                                                                          SCOP domains
               CATH domains 2vrfB00 B:-1-204  [code=2.30.42.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee....e------eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: B:115-198 UniProt: 115-198                                                ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2vrf B  -1 SMPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVN------TVV 204
                             ||    119       129       139       149       159       169       179       189       199 |     203 
                             0|                                                                                      201    202  
                            112                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with SNTB2_HUMAN | Q13425 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:101
                                   119       129       139       149       159       169       179       189       199       209 
          SNTB2_HUMAN   110 SPPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVTPYIKKPSLV 210
               SCOP domains d2vrfc_ C: automated matches                                                                          SCOP domains
               CATH domains 2vrfC00 C:-1-204  [code=2.30.42.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.....------eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: C:115-198 UniProt: 115-198                                                ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2vrf C  -1 SMPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVN------TVV 204
                             ||    119       129       139       149       159       169       179       189       199 |     203 
                             0|                                                                                      201    202  
                            112                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with SNTB2_HUMAN | Q13425 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:101
                                   119       129       139       149       159       169       179       189       199       209 
          SNTB2_HUMAN   110 SPPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVTPYIKKPSLV 210
               SCOP domains d2vrfd_ D: automated matches                                                                          SCOP domains
               CATH domains 2vrfD00 D:-1-204  [code=2.30.42.10, no name defined]                                                  CATH domains
           Pfam domains (1) -----PDZ-2vrfD01 D:115-195                                                            --------------- Pfam domains (1)
           Pfam domains (2) -----PDZ-2vrfD02 D:115-195                                                            --------------- Pfam domains (2)
           Pfam domains (3) -----PDZ-2vrfD03 D:115-195                                                            --------------- Pfam domains (3)
           Pfam domains (4) -----PDZ-2vrfD04 D:115-195                                                            --------------- Pfam domains (4)
         Sec.struct. author ...eeeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.....------eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: D:115-198 UniProt: 115-198                                                ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2vrf D  -1 SMPVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGLAADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAGKEVLLEVKFIREVN------TVV 204
                             ||    119       129       139       149       159       169       179       189       199 |     203 
                             0|                                                                                      201    202  
                            112                                                                                                  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-2vrfD01D:115-195
1bPDZ-2vrfD02D:115-195
1cPDZ-2vrfD03D:115-195
1dPDZ-2vrfD04D:115-195

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SNTB2_HUMAN | Q13425)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0016010    dystrophin-associated glycoprotein complex    A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

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