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(-) Description

Title :  CRYSTAL STRUCTURE OF T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN QUADRUPLE MUTANT (QM) IN COMPLEX WITH CASPR4 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 :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Beta Barrel Fold Protein, Pdz Domain; Peptide Binding, Specificity Mutant, Scaffold Signaling Protein For Cell Adhesion And Cell Junction, Signaling Domain, Protein-Peptide Complex, 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
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A-6HIS-RTEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Gene: TIAM1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HUMAN
    Synonym: TIAM-1
 
Molecule 2 - CONTACTIN-ASSOCIATED PROTEIN-LIKE 4 PEPTIDE
    Chains: D, E, F
    Engineered: YES
    Fragment: UNP RESIDUES 1301-1308
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CASPR4 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NXQ)

(-) Sites  (0, 0)

(no "Site" information available for 4NXQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NXQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh......eeeeeeee..eeeeeeeee...hhhhhh......eeeee..ee.hhhhhhhhhhhhhh.eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4nxq A 839 MGKVTHSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMMEDFFSQPSVGLLVRTYPE 929
                                   848       858       868       878       888       898       908       918       928 


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


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


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               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 ------- Transcript
                 4nxq D   2 NQKEYFF   8


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               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 ------ Transcript
                 4nxq E   3 QKEYFF   8


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               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 ------ Transcript
                 4nxq F   3 QKEYFF   8
   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 4NXQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (62, 66)

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  TIAM1_HUMAN | Q13009
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 Related Entries

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

UniProtKB/Swiss-Prot
        TIAM1_HUMAN | Q13009: 2d8i 3kzd 3kze 4gvc 4gvd 4k2o 4k2p 4nxp 4nxr

(-) 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
4nxr