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(-) Description

Title :  SOLUTION STRUCTURE OF THE AF-6 PDZ DOMAIN COMPLEXED WITH THE C-TERMINAL PEPTIDE FROM THE BCR PROTEIN
 
Authors :  Q. Chen, J. Wu, Y. Shi
Date :  30 Jul 05  (Deposition) - 18 Jul 06  (Release) - 19 Jan 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Af-6 Pdz Domain/Bcr Complex, Cell Adhesion/Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Chen, X. Niu, Y. Xu, J. Wu, Y. Shi
Solution Structure And Backbone Dynamics Of The Af-6 Pdz Domain/Bcr Peptide Complex.
Protein Sci. V. 16 1053 2007
PubMed-ID: 17473018  |  Reference-DOI: 10.1110/PS.062440607
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AFADIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B (+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: AF-6 PDZ DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AF-6 PROTEIN
 
Molecule 2 - 6-MER PEPTIDE FROM BREAKPOINT CLUSTER REGION PROTEIN
    Chains: B
    EC Number: 2.7.1.-
    Engineered: YES
    Fragment: C-TERMINAL PEPTIDE
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2AIN)

(-) Sites  (0, 0)

(no "Site" information available for 2AIN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.AFAD_HUMAN1007-1093  1A:6-92

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003058772aENSE00001897802chr22:23522397-235244262030BCR_HUMAN1-4274270--
1.8bENST000003058778bENSE00001683705chr22:23595986-23596167182BCR_HUMAN427-487610--
1.9ENST000003058779ENSE00001602182chr22:23603137-23603241105BCR_HUMAN488-522350--
1.10eENST0000030587710eENSE00001658624chr22:23603542-23603727186BCR_HUMAN523-584620--
1.11ENST0000030587711ENSE00001154392chr22:23610595-23610702108BCR_HUMAN585-620360--
1.12ENST0000030587712ENSE00001801315chr22:23613719-2361377961BCR_HUMAN621-641210--
1.13ENST0000030587713ENSE00001689593chr22:23615268-2361532053BCR_HUMAN641-658180--
1.14aENST0000030587714aENSE00001755753chr22:23615821-23615961141BCR_HUMAN659-705470--
1.15cENST0000030587715cENSE00001616269chr22:23626164-23626285122BCR_HUMAN706-746410--
1.16bENST0000030587716bENSE00002165169chr22:23627220-23627388169BCR_HUMAN746-802570--
1.17bENST0000030587717bENSE00001634720chr22:23629346-23629465120BCR_HUMAN803-842400--
1.18ENST0000030587718ENSE00001799418chr22:23630284-2363035976BCR_HUMAN843-868260--
1.19aENST0000030587719aENSE00001654687chr22:23631704-23631808105BCR_HUMAN868-903360--
1.19dENST0000030587719dENSE00001781765chr22:23632526-2363260075BCR_HUMAN903-928260--
1.20ENST0000030587720ENSE00001720909chr22:23634728-2363482598BCR_HUMAN928-960330--
1.21aENST0000030587721aENSE00001775681chr22:23637211-23637342132BCR_HUMAN961-1004440--
1.26aENST0000030587726aENSE00001617680chr22:23651611-2365167060BCR_HUMAN1005-1024200--
1.26dENST0000030587726dENSE00001728146chr22:23652511-23652620110BCR_HUMAN1025-1061370--
1.27aENST0000030587727aENSE00001664359chr22:23653884-23654023140BCR_HUMAN1061-1108480--
1.28bENST0000030587728bENSE00001718886chr22:23655074-23655208135BCR_HUMAN1108-1153460--
1.29bENST0000030587729bENSE00001759350chr22:23656155-23656260106BCR_HUMAN1153-1188360--
1.30bENST0000030587730bENSE00001741269chr22:23656739-23656901163BCR_HUMAN1188-1242550--
1.31eENST0000030587731eENSE00001753733chr22:23657620-236602242605BCR_HUMAN1243-1271291B:99-1046

(-) Sequences/Alignments

NMR Structure
   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:93
 aligned with AFAD_HUMAN | P55196 from UniProtKB/Swiss-Prot  Length:1824

    Alignment length:93
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091   
          AFAD_HUMAN   1002 RKEPEIITVTLKKQNGMGLSIVAAKGAGQDKLGIYVKSVVKGGAADVDGRLAAGDQLLSVDGRSLVGLSQERAAELMTRTSSVVTLEVAKQGA 1094
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ainA00 A:1-93  [code=2.30.42.10, no name defined]                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee......eeeeee........eeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:6-92 UniProt: 1007-1093                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                2ain A    1 MKEPEIITVTLKKQNGMGLSIVAAKGAGQDKLGIYVKSVVKGGAADVDGRLAAGDQLLSVDGRSLVGLSQERAAELMTRTSSVVTLEVAKQGA   93
                                    10        20        30        40        50        60        70        80        90   


Chain B from PDB  Type:PROTEIN  Length:6
 aligned with BCR_HUMAN | P11274 from UniProtKB/Swiss-Prot  Length:1271

    Alignment length:6
           BCR_HUMAN   1266 LFSTEV 1271
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
               Transcript 1 1.31e  Transcript 1
                2ain B   99 LFSTEV  104
   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 2AIN)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AIN)

(-) Gene Ontology  (53, 60)

NMR Structure(hide GO term definitions)
Chain A   (AFAD_HUMAN | P55196)
molecular function
    GO:0017016    Ras GTPase binding    Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0090557    establishment of endothelial intestinal barrier    The establishment of a barrier between endothelial cell layers of the intestine to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain B   (BCR_HUMAN | P11274)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0060313    negative regulation of blood vessel remodeling    Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0002692    negative regulation of cellular extravasation    Any process that stops, prevents, or reduces the frequency, rate, or extent of cellular extravasation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0043314    negative regulation of neutrophil degranulation    Any process that stops, prevents, or reduces the rate of neutrophil degranulation.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0043114    regulation of vascular permeability    Any process that modulates the extent to which blood vessels can be pervaded by fluid.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving 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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AFAD_HUMAN | P55196: 1t2m 1xz9 2exg 5a6c
        BCR_HUMAN | P11274: 1k1f

(-) Related Entries Specified in the PDB File

1t2m SOLUTION STRUCTURE OF THE AF-6 PDZ DOMAIN