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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TPR DOMAIN OF LGN IN COMPLEX WITH FRMPD4/PRESO1 AT 1.5 ANGSTROM RESOLUTION
 
Authors :  H. Takayanagi, S. Yuzawa, H. Sumimoto
Date :  11 Oct 14  (Deposition) - 16 Sep 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tetratricopeptide Repeat, Tpr, Cell Polarity, Cytoplasm And Cell Cortex, Signaling Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takayanagi, S. Yuzawa, H. Sumimoto
Structural Basis For The Recognition Of The Scaffold Protei Frmpd4/Preso1 By The Tpr Domain Of The Adaptor Protein Lgn
Acta Crystallogr. , Sect. F V. 71 175 2015
PubMed-ID: 25664792  |  Reference-DOI: 10.1107/S2053230X14028143

(-) Compounds

Molecule 1 - G-PROTEIN-SIGNALING MODULATOR 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSFDUET-1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL TPR DOMAIN, UNP RESIDUES 20-421
    Gene: GPSM2, LGN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MOSAIC PROTEIN LGN
 
Molecule 2 - FERM AND PDZ DOMAIN-CONTAINING PROTEIN 4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-6P-2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FRMPD4-L, UNP RESIDUES 978-1025
    Gene: FRMPD4, KIAA0316, PDZD10, PDZK10
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PDZ DOMAIN-CONTAINING PROTEIN 10,PSD-95-INTERACTING REGULATOR OF SPINE MORPHOGENESIS,PRESO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SCN7Ligand/IonTHIOCYANATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:82 , SER A:98 , HOH A:628binding site for residue SCN A 501
02AC2SOFTWAREGLY A:109 , ASN A:110 , GLU A:113binding site for residue SCN A 502
03AC3SOFTWAREGLU A:179 , PHE A:198 , LEU A:201 , PGE A:513 , HOH A:608binding site for residue SCN A 503
04AC4SOFTWARELYS A:231 , ALA A:232 , ARG A:235 , LEU A:268 , HOH A:669binding site for residue SCN A 504
05AC5SOFTWAREARG A:266 , LEU A:268 , ARG A:271 , GLU A:274 , HOH A:746binding site for residue SCN A 505
06AC6SOFTWAREGLN A:119 , ARG A:126 , HOH A:771binding site for residue SCN A 506
07AC7SOFTWAREGLU A:25 , ARG A:26 , HOH A:647binding site for residue SCN A 507
08AC8SOFTWARELYS A:106 , ASN A:143 , HIS A:146 , LYS A:150 , HOH A:768 , GLU B:1000binding site for residue PEG A 508
09AC9SOFTWARESER A:151 , PHE A:152binding site for residue PEG A 509
10AD1SOFTWAREHIS A:341 , LEU B:990binding site for residue PEG A 510
11AD2SOFTWARETYR A:145 , LYS A:148 , ASP A:169 , ALA A:170 , HOH A:606 , HOH A:744 , HOH A:749binding site for residue PEG A 511
12AD3SOFTWAREALA A:275 , GLN A:276 , TYR A:279 , HIS A:301 , ASP A:310 , ARG A:316 , HOH A:802binding site for residue PEG A 512
13AD4SOFTWAREARG A:34 , ALA A:35 , SER A:38 , PHE A:39 , THR A:186 , GLN A:194 , PHE A:198 , GLN A:220 , SCN A:503 , HOH A:619 , HOH A:645 , HOH A:678binding site for residue PGE A 513
14AD5SOFTWARETYR A:206 , LEU A:207 , PHE A:211 , PHE A:247binding site for residue EDO A 514
15AD6SOFTWAREHIS A:79 , HIS A:80 , THR A:83 , HOH A:620 , HOH A:735binding site for residue EDO A 515
16AD7SOFTWAREGLU A:256 , LYS A:260binding site for residue EDO A 516
17AD8SOFTWARELYS A:148 , PHE A:152 , HOH A:749binding site for residue EDO A 517
18AD9SOFTWAREGLN A:289 , ASP A:290 , TYR A:291 , GLU A:292binding site for residue EDO A 518
19AE1SOFTWAREGLU A:113 , VAL A:116 , CYS A:117 , HOH A:615 , HOH A:628binding site for residue EDO A 519

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WND)

(-) 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
(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:329
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wnd A   13 MEASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVG  349
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152 ||    170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
                                                                                                                                                                       154|                                                                                                                                                                                          
                                                                                                                                                                        163                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:26
                                                           
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..................hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                4wnd B  988 QLLHSDHMEMEPETMETKSVTDYFSK 1013
                                   997      1007
   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 4WND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4wnd
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  GPSM2_HUMAN | P81274
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 Related Entries

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

UniProtKB/Swiss-Prot
        FRPD4_HUMAN | Q14CM0: 4wne 4wnf 4wng
        GPSM2_HUMAN | P81274: 3sf4 4wne 4wnf 4wng 5a6c

(-) Related Entries Specified in the PDB File

3sf4 3SF4 CONTAINS THE SAME PROTEIN COMPLEXED WITH MINSC.
4wne
4wnf
4wng