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(-) Description

Title :  CRYSTAL STRUCTURE OF T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN QUADRUPLE MUTANT (QM) IN COMPLEX WITH NEUREXIN-1 PEPTIDE
 
Authors :  X. Liu, D. C. Speckhard, T. R. Shepherd, S. R. Hengel, E. J. Fuentes
Date :  09 Dec 13  (Deposition) - 13 May 15  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel Fold Protein, Pdz Domain, Peptide Binding, Specificity Mutant, Scaffold Signaling Protein For Cell Adhesion And Cell Junction, Signaling Domain, Signaling Protein-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Liu, D. C. Speckhard, T. R. Shepherd, Y. J. Sun, S. R. Hengel, L. Yu, C. A. Fowler, L. Gakhar, E. J. Fuentes
Distinct Roles For Conformational Dynamics In Protein-Ligan Interactions.
Structure V. 24 2053 2016
PubMed-ID: 27998539  |  Reference-DOI: 10.1016/J.STR.2016.08.019

(-) Compounds

Molecule 1 - T-LYMPHOMA INVASION AND METASTASIS-INDUCING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A-6HIS-RTEV
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneTIAM1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainHUMAN
    SynonymTIAM-1
 
Molecule 2 - NEUREXIN-2-BETA PEPTIDE
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUE 659-666
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEUREXIN II-BETA PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ANS1Ligand/Ion5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYLACID)
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:838 , ASP A:868 , GLY A:869 , LYS A:879 , GLU A:897 , ASN A:900 , TYR A:927 , HOH A:1146 , HOH A:1161 , HOH A:1181 , TYR B:7 , HOH B:203BINDING SITE FOR RESIDUE EPE A 1001
2AC2SOFTWAREARG A:901 , ASN A:907 , SER A:909 , ASP A:913 , PHE A:914 , ASN B:1BINDING SITE FOR RESIDUE ANS B 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NXR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NXR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NXR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NXR)

(-) Exons   (0, 0)

(no "Exon" information available for 4NXR)

(-) Sequences/Alignments

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhh.......eeeeeee..eeeeeee.....hhhhhh......eeeee..ee.hhhhhhhhhhhhhh.eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4nxr A 837 GAMGKVTHSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMMEDFFSQPSVGLLVRTYPEL 930
                                   846       856       866       876       886       896       906       916       926    

Chain B from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .eeeeee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4nxr B   1 NKDKEYYV   8

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  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 4NXR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NXR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NXR)

(-) Gene Ontology  (63, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TIAM1_HUMAN | Q130092d8i 3kzd 3kze 4gvc 4gvd 4k2o 4k2p 4nxp 4nxq

(-) Related Entries Specified in the PDB File

3kzd THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE IN APO STATE
3kze THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE IN MODEL PEPTIDE-BOUND STATE
4gvc THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE IN PSDC1-BOUND STATE
4gvd THE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN WILD TYPE IN SDC1-BOUND STATE
4nxp
4nxq