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(-) Description

Title :  COMPLEX STRUCTURE OF NORRIN WITH HUMAN FRIZZLED 4
 
Authors :  Z. Wang, J. Ke, G. Shen, Z. Cheng, H. E. Xu, W. Xu
Date :  16 Jul 15  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Wnt, Norrin, Frizzled, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Shen, J. Ke, Z. Wang, Z. Cheng, X. Gu, Y. Wei, K. Melcher, H. E. Xu, W. Xu
Structural Basis Of The Norrin-Frizzled 4 Interaction.
Cell Res. V. 25 1078 2015
PubMed-ID: 26227961  |  Reference-DOI: 10.1038/CR.2015.92

(-) Compounds

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN,NORRIN
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP Q00604 RESIDUES 31-133
    Gene: MALE, Z5632, ECS5017, NDP, EVR2
    Organism Common: HUMAN
    Organism Taxid: 83334, 9606
    Synonym: MBP,MMBP,MALTODEXTRIN-BINDING PROTEIN,NORRIE DISEASE PROTEIN,X-LINKED EXUDATIVE VITREORETINOPATHY 2 PROTEIN
 
Molecule 2 - FRIZZLED-4
    Chains: C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 38-160
    Gene: FZD4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HFZ4,FZE4

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:59binding site for residue NAG C 201
2AC2SOFTWAREASN C:144 , LYS D:133binding site for residue NAG C 202
3AC3SOFTWAREASN D:59binding site for residue NAG D 201
4AC4SOFTWAREASN D:144 , SER D:146binding site for residue NAG D 202

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:1039 -A:1096
2A:1055 -A:1110
3A:1065 -A:1126
4A:1069 -A:1128
5A:1093 -B:1095
6A:1095 -B:1093
7A:1131 -B:1131
8B:1039 -B:1096
9B:1055 -B:1110
10B:1065 -B:1126
11B:1069 -B:1128
12C:45 -C:106
13C:53 -C:99
14C:90 -C:128
15C:117 -C:158
16C:121 -C:145
17D:45 -D:106
18D:53 -D:99
19D:90 -D:128
20D:117 -D:158
21D:121 -D:145

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met C:63 -Pro C:64
2Met D:63 -Pro D:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CL1)

(-) Exons   (0, 0)

(no "Exon" information available for 5CL1)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhh.......hhhhhhhhhhhhhhh.ee..ee.eee.ee...eeeee............hhhhhhhhhhh...eee.....hhhhhhhhhhhhh....ee....ee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee............ee..eeeee.....hhhhhhhhhhh...hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..........eeeeeeeee.........eeeeeeeeee.....eeeee.ee........eeee.eeeeeeeeeee...............eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cl1 A    1 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 1133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370|     1041      1051      1061      1071      1081      1091      1101      1111      1121      1131  
                                                                                                                                                                                                                                                                                                                                                                                                           370|                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                           1032                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhh.......hhhhhhhhhhhhhhh.ee..ee.eee.ee...eeeee............hhhhhhhhhhh...eee.....hhhhhhhhhhhhh....ee....ee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee...ee..ee...ee..eeeee.....hhhhhhhhhhh...hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........eeeeeeeee.........eeeeeeeeee.....eeeee...........eeee.eeeeeeeeeee..ee.......ee.eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cl1 B    1 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAASDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS 1133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370|     1043      1053      1063      1073      1083      1093      1103      1113      1123      1133
                                                                                                                                                                                                                                                                                                                                                                                                           370|                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                           1034                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:117
                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee............ee.........hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhh...........eehhhhhhhhhhhhhhhhhhh....hhhhh.............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                5cl1 C   44 RCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCME  160
                                    53        63        73        83        93       103       113       123       133       143       153       


Chain D from PDB  Type:PROTEIN  Length:118
                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee............ee.........hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh....hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                5cl1 D   43 RRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCME  160
                                    52        62        72        82        92       102       112       122       132       142       152
   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 5CL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CL1)

(-) Gene Ontology  (64, 75)

Asymmetric/Biological Unit(hide GO term definitions)

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  5cl1
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 Related Entries

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

UniProtKB/Swiss-Prot
        FZD4_HUMAN | Q9ULV1: 5bpb 5bpq 5bqc 5bqe 5cm4 5uwg
        MALE_ECO57 | P0AEY0: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2v93 3io4 3io6 3mbp 3osq 3osr 3vd8 4feb 4mbp 4my2 4wgi 4wrn 4wth 4wvg 4wvh 4wvi 4wvj 4xa2 4xai 4xaj 4xhs 4ys9 5bmy 5c7r 5dfm 5e24 5e7u 5edu 5fio 5ii4 5jj4 5jon 5jtq 5jtr 5k94 5ldf 5lof 5t03 5t05 5t0a 5ttd
        NDP_HUMAN | Q00604: 4my2 5bpu 5bq8 5bqb 5bqc 5bqe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CL1)