Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF NORRIN IN COMPLEX WITH THE CYSTEINE-RICH DOMAIN OF FRIZZLED 4 -METHYLATED FORM
 
Authors :  T. -H. Chang, F. -L. Hsieh, K. Harlos, E. Y. Jones
Date :  28 May 15  (Deposition) - 01 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A (1x),B (1x),C (2x)
Keywords :  Wnt Signalling Pathway, Norrie Disease Protein, Glycoprotein, G Protein Coupled Receptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. H. Chang, F. L. Hsieh, M. Zebisch, K. Harlos, J. Elegheert, E. Y. Jone
Structure And Functional Properties Of Norrin Mimic Wnt For Signalling With Frizzled4, Lrp5/6, And Proteoglycan.
Elife V. 4 06554 2015
PubMed-ID: 26158506  |  Reference-DOI: 10.7554/ELIFE.06554

(-) Compounds

Molecule 1 - NORRIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Atcc NumberCRL-11268
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLIGK-STR-8H-SUMO-1D4
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentRESIDUES 25-133
    GeneNDP, EVR2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNORRIE DISEASE PROTEIN,X-LINKED EXUDATIVE VITREORETINOPATHY 2 PROTEIN
 
Molecule 2 - NORRIN
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Atcc NumberCRL-11268
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLIGK-STR-8H-SUMO-1D4
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentRESIDUES 25-133
    GeneNDP, EVR2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNORRIE DISEASE PROTEIN,X-LINKED EXUDATIVE VITREORETINOPATHY 2 PROTEIN
 
Molecule 3 - FRIZZLED-4
    ChainsC
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Atcc NumberCRL-11268
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC-MVENUS-12H
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentRESIDUES 42-179
    GeneFZD4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHFZ4,FZE4

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)A (1x)B (1x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG03Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG04Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE C:135binding site for residue PG0 B 201
2AC2SOFTWARELEU A:103 , THR A:119 , ARG A:121 , LEU B:78 , SER B:80 , MLY B:86 , GLN B:87 , PRO B:88binding site for residue PG0 B 202
3AC3SOFTWARESER C:92binding site for residue CL C 202
4AC4SOFTWARECYS C:117 , GLY C:119 , MET C:120 , SER C:123 , GLU C:160 , GLY C:161 , PRO C:162 , GLY C:163binding site for residue PG0 C 203
5AC5SOFTWARETHR B:117 , GLU C:141 , ASN C:144 , SER C:146binding site for Mono-Saccharide NAG C 201 bound to ASN C 144

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:39 -A:96
2A:55 -A:110
3A:65 -A:126
4A:69 -A:128
5A:93 -B:95
6A:95 -B:93
7A:131 -B:131
8B:39 -B:96
9B:55 -B:110
10B:65 -B:126
11B:69 -B:128
12C:45 -C:106
13C:53 -C:99
14C:90 -C:128
15C:117 -C:158
16C:121 -C:145

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met C:63 -Pro C:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BQE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BQE)

(-) Exons   (0, 0)

(no "Exon" information available for 5BQE)

(-) Sequences/Alignments

Asymmetric 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:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5bqe A  33 DSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    42        52        62        72        82        92       102       112       122       132 

Chain B from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeee.........eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5bqe B  33 DSDPRRCMRHHYVDSISHPLYKCSSkMVLLARCEGHCSQASRSEPLVSFSTVLkQPFRSSCHCCRPQTSkLkALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    42        52     |  62        72        82   |    92       102 |     112       122       132 
                                                    58-MLY                      86-MLY         102-MLY                           
                                                                                                 104-MLY                         

Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhh.....ee.........hhhhhhhhhh.hhhhhhh....hhhhhhhhhhh...........eehhhhhhhhhhhhhhhhhhh....hhhhhhhhh.........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqe C  43 RRCDPIRISMCQNLGYNVTkMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVkRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGPGD 164
                                    52        62        72        82        92       102       112       122  |    132       142       152       162  
                                              62-MLY                                                        125-MLY                                   

   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 5BQE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BQE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BQE)

(-) Gene Ontology  (58, 69)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG0  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met C:63 - Pro C:64   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5bqe
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FZD4_HUMAN | Q9ULV1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  NDP_HUMAN | Q00604
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FZD4_HUMAN | Q9ULV1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NDP_HUMAN | Q00604
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FZD4_HUMAN | Q9ULV15bpb 5bpq 5bqc 5cl1 5cm4 5uwg
        NDP_HUMAN | Q006044my2 5bpu 5bq8 5bqb 5bqc 5cl1

(-) Related Entries Specified in the PDB File

5bpb HUMAN FRIZZLED 4 CYSTEINE-RICH DOMAIN CRYSTAL FORM I
5bpq HUMAN FRIZZLED 4 CYSTEINE-RICH DOMAIN CRYSTAL FORM II
5bpu HUMAN NORRIN STRUCTURE CRYSTAL FORM I
5bq8 UMAN NORRIN STRUCTURE CRYSTAL FORM II
5bqb HUMAN NORRIN STRUCTURE CRYSTAL FORM III
5bqc NORRIN IN COMPLEX WITH THE CYSTEINE-RICH DOMAIN OF FRIZZLED 4 AND SUCROSE OCTASULFATE