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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF HUMAN FRIZZLED 4 - CRYSTAL FORM I
 
Authors :  T. -H. Chang, F. -L. Hsieh, K. Harlos, E. Y. Jones
Date :  27 May 15  (Deposition) - 01 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  D  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Wnt Signalling Pathway, Glycoprotein, G Protein Coupled Receptor, Receptor For Norrin Recognition, 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 - FRIZZLED-4
    Chains: A, B, D, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC-MVENUS-12H
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 42-179
    Gene: FZD4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HFZ4,FZE4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):    D
Biological Unit 4 (1x):   C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:59binding site for Mono-Saccharide NAG A 202 bound to ASN A 59
2AC2SOFTWAREGLU A:141 , ASN A:144binding site for Mono-Saccharide NAG A 201 bound to ASN A 144
3AC3SOFTWAREASN B:59binding site for Mono-Saccharide NAG B 202 bound to ASN B 59
4AC4SOFTWAREGLU B:141 , ASN B:144 , SER B:146 , LEU D:169 , HIS D:171binding site for Mono-Saccharide NAG B 201 bound to ASN B 144
5AC5SOFTWAREGLU D:141 , ASN D:144binding site for Mono-Saccharide NAG D 201 bound to ASN D 144

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:45 -A:106
2A:53 -A:99
3A:90 -A:128
4A:117 -A:158
5A:121 -A:145
6B:45 -B:106
7B:53 -B:99
8B:90 -B:128
9B:117 -B:158
10B:121 -B:145
11C:45 -C:106
12C:53 -C:99
13C:90 -C:128
14C:117 -C:158
15C:121 -C:145
16D:45 -D:106
17D:53 -D:99
18D:90 -D:128
19D:117 -D:158
20D:121 -D:145

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:63 -Pro A:64
2Met B:63 -Pro B:64
3Met D:63 -Pro D:64
4Met C:63 -Pro C:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BPB)

(-) 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:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee.........hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhh.eee..eeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpb A  44 RCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGP 162
                                    53        63        73        83        93       103       113       123       133       143       153         


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee.........hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhh.eee..eeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpb B  44 RCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGPGDELEVLF 186
                                    53        63        73        83        93       103       113       123       133       143       153       163 ||    
                                                                                                                                                   165|    
                                                                                                                                                    182    


Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee.........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpb C  44 RCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEG 161
                                    53        63        73        83        93       103       113       123       133       143       153        


Chain D from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhh.....ee.........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpb D  43 RRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGPGDEEVPLPHK 172
                                    52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
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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 5BPB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        FZD4_HUMAN | Q9ULV1: 5bpq 5bqc 5bqe 5cl1 5cm4 5uwg

(-) Related Entries Specified in the PDB File

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