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(-) Description

Title :  CRYSTAL STRUCTURE OF NORRIN, A WNT SIGNALLING ACTIVATOR, CRYSTAL FORM I
 
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 :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,H,I
Biol. Unit 1:  A,B,H  (1x)
Biol. Unit 2:  C,D,H,I  (1x)
Biol. Unit 3:  E,F,I  (1x)
Keywords :  Wnt Signalling Pathway, Norrie Disease Protein, Cystine-Knot Like Growth Factor, Ligand For Frizzled 4 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
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLIGK-STR-8H-SUMO-1D4
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 25-133
    Gene: NDP, EVR2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NORRIE DISEASE PROTEIN,X-LINKED EXUDATIVE VITREORETINOPATHY 2 PROTEIN
 
Molecule 2 - (GGL)EEEEEE
    Chains: H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - (GGL)EEE
    Chains: I
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHI
Biological Unit 1 (1x): AB    H 
Biological Unit 2 (1x):   CD  HI
Biological Unit 3 (1x):     EF I

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GGL2Mod. Amino AcidGAMMA-L-GLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GGL1Mod. Amino AcidGAMMA-L-GLUTAMIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GGL2Mod. Amino AcidGAMMA-L-GLUTAMIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GGL1Mod. Amino AcidGAMMA-L-GLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 5BPU)

(-) SS Bonds  (33, 33)

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:39 -C:96
13C:55 -C:110
14C:65 -C:126
15C:69 -C:128
16C:93 -D:95
17C:95 -D:93
18C:131 -D:131
19D:39 -D:96
20D:55 -D:110
21D:65 -D:126
22D:69 -D:128
23E:39 -E:96
24E:55 -E:110
25E:65 -E:126
26E:69 -E:128
27E:93 -F:95
28E:95 -F:93
29E:131 -F:131
30F:39 -F:96
31F:55 -F:110
32F:65 -F:126
33F:69 -F:128

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly E:112 -Gly E:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BPU)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5bpu A  31 IMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNSGTETSQVA 141
                                    40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5bpu B  35 DPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    44        54        64        74        84        94       104       114       124         


Chain C from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5bpu C  33 DSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNSGT 135
                                    42        52        62        72        82        92       102       112       122       132   


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               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
                 5bpu D  32 MDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    41        51        61        71        81        91       101       111       121       131  


Chain E from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......ee.eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5bpu E  34 SDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    43        53        63        73        83        93       103       113       123       133


Chain F from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               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
                 5bpu F  35 DPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 133
                                    44        54        64        74        84        94       104       114       124         


Chain H from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5bpu H   1 xEEEEEE   7
                            |      
                            1-GGL  


Chain I from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5bpu I   1 xEEE   4
                            |   
                            1-GGL
   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 5BPU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

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    Gly E:112 - Gly E:113   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        NDP_HUMAN | Q00604: 4my2 5bq8 5bqb 5bqc 5bqe 5cl1

(-) Related Entries Specified in the PDB File

4my2 4MY2 CONTAINS THE SAME PROTEIN FUSED WITH MALTOSE-BINDING PERIPLASMIC PROTEIN.