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(-) Description

Title :  CD2BP2-GYF DOMAIN IN COMPLEX WITH PROLINE-RICH CD2 TAIL SEGMENT PEPTIDE
 
Authors :  C. Freund, R. Kuhne, H. Yang, S. Park, E. L. Reinherz, G. Wagner
Date :  26 Feb 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (15x)
Keywords :  Gyf Domain, Protein-Protein Interaction, Proline-Rich Peptide, Cd2, Cd2Bp2, Peptide Binding/Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Freund, R. Kuhne, H. Yang, S. Park, E. L. Reinherz, G. Wagner
Dynamic Interaction Of Cd2 With The Gyf And The Sh3 Domain Of Compartmentalized Effector Molecules
Embo J. V. 21 5985 2002
PubMed-ID: 12426371  |  Reference-DOI: 10.1093/EMBOJ/CDF602
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPTFT74
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUE 1-62
    GeneCD2BP2 (AMINO ACIDS 280-341)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - T-CELL SURFACE ANTIGEN CD2
    ChainsB
    EngineeredYES
    FragmentRESIDUE 63-73
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymT-CELL SURFACE ANTIGEN T11/LEU-5, LFA-2, LFA-3 RECEPTOR, ERYTHROCYTE RECEPTOR, ROSETTE RECEPTOR
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1L2Z)

(-) Sites  (0, 0)

(no "Site" information available for 1L2Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L2Z)

(-) Cis Peptide Bonds  (1, 15)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Asp A:44 -Pro A:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L2Z)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GYFPS50829 GYF domain profile.CD2B2_HUMAN280-338  1A:1-59

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003055961ENSE00001389090chr16:30366682-30366533150CD2B2_HUMAN-00--
1.2ENST000003055962ENSE00001328785chr16:30366028-30365925104CD2B2_HUMAN1-26260--
1.3ENST000003055963ENSE00001139812chr16:30365643-30365505139CD2B2_HUMAN27-73470--
1.4ENST000003055964ENSE00001139805chr16:30365379-30365222158CD2B2_HUMAN73-125530--
1.5ENST000003055965ENSE00001139799chr16:30365121-30364689433CD2B2_HUMAN126-2701450--
1.6ENST000003055966ENSE00001139794chr16:30364608-30364502107CD2B2_HUMAN270-305361A:1-2626
1.7ENST000003055967ENSE00001316361chr16:30364416-303620872330CD2B2_HUMAN306-341361A:27-6236

2.1aENST000003694781aENSE00001450130chr1:117297007-117297175169CD2_HUMAN1-21210--
2.2aENST000003694782aENSE00000785006chr1:117297253-117297573321CD2_HUMAN21-1281080--
2.3ENST000003694783ENSE00000785007chr1:117303024-117303254231CD2_HUMAN128-205780--
2.4ENST000003694784ENSE00000785008chr1:117307106-117307228123CD2_HUMAN205-246420--
2.5ENST000003694785ENSE00001141790chr1:117311086-117311850765CD2_HUMAN246-3511061B:63-7311

(-) 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:62
 aligned with CD2B2_HUMAN | O95400 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:62
                                   289       299       309       319       329       339  
          CD2B2_HUMAN   280 DVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT 341
               SCOP domains d1l2za_ A: GYF domain from cd2bp2 protein                      SCOP domains
               CATH domains 1l2zA00 A:1-62  [code=3.30.1490.40, no name defined]           CATH domains
               Pfam domains -GYF-1l2zA01 A:2-59                                        --- Pfam domains
         Sec.struct. author ....eee.............hhhhhhhhhhhh......eee.........ee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GYF  PDB: A:1-59 UniProt: 280-338                          --- PROSITE
               Transcript 1 Exon 1.6  PDB: A:1-26     Exon 1.7  PDB: A:27-62               Transcript 1
                 1l2z A   1 DVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT  62
                                    10        20        30        40        50        60  

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with CD2_HUMAN | P06729 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:11
                                   303 
            CD2_HUMAN   294 SHRPPPPGHRV 304
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
               Transcript 2 Exon 2.5    Transcript 2
                 1l2z B  63 SHRPPPPGHRV  73
                                    72 

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (40, 41)

NMR Structure(hide GO term definitions)
Chain A   (CD2B2_HUMAN | O95400)
molecular function
    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:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0000244    spliceosomal tri-snRNP complex assembly    The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
    GO:0046540    U4/U6 x U5 tri-snRNP complex    A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain B   (CD2_HUMAN | P06729)
molecular function
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0001766    membrane raft polarization    The clustering and aggregation of membrane rafts at a single cellular pole during activation of particular cell types, such as lymphocytes.
    GO:0030101    natural killer cell activation    The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:1902715    positive regulation of interferon-gamma secretion    Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
    GO:2000484    positive regulation of interleukin-8 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
    GO:0030887    positive regulation of myeloid dendritic cell activation    Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0045580    regulation of T cell differentiation    Any process that modulates the frequency, rate or extent of T cell differentiation.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0046658    anchored component of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD2B2_HUMAN | O954001gyf 1syx 4bws
        CD2_HUMAN | P067291cdb 1gya 1hnf 1qa9 2j6o 2j7i

(-) Related Entries Specified in the PDB File

1gyf GYF DOMAIN FROM HUMAN CD2BP2 PROTEIN