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(-) Description

Title :  CRYSTAL STRUCTURE OF GDF8
 
Authors :  R. G. Walker, T. B. Thompson
Date :  21 Apr 16  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gdf8, Myostatin, Tgfbeta, Ligand, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. G. Walker, M. Czepnik, E. J. Goebel, J. C. Mccoy, A. Vujic, M. Cho, J. Oh, S. Aykul, K. L. Walton, G. Schang, D. J. Bernard, A. P. Hinck, C. A. Harrison, E. Martinez-Hackert, A. J. Wagers, R. T. Lee, T. B. Thompson
Structural Basis For Potency Differences Between Gdf8 And Gdf11.
Bmc Biol. V. 15 19 2017
PubMed-ID: 28257634  |  Reference-DOI: 10.1186/S12915-017-0350-1

(-) Compounds

Molecule 1 - GROWTH/DIFFERENTIATION FACTOR 8
    ChainsA, B
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellCHO
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    FragmentUNP RESIDUES 268-376
    GeneMSTN, GDF8
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymGDF-8,MYOSTATIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:31 , MET A:84binding site for residue MPD A 201
2AC2SOFTWAREPRO A:76 , LYS A:78 , MET A:79binding site for residue MPD A 202
3AC3SOFTWAREALA A:34 , PRO A:35 , LYS A:36 , MPD A:204 , ARG B:14binding site for residue MPD A 203
4AC4SOFTWAREMPD A:203binding site for residue MPD A 204
5AC5SOFTWAREALA B:26 , PHE B:27 , LYS B:78 , MET B:79binding site for residue MPD B 201
6AC6SOFTWAREMET B:84binding site for residue MPD B 202
7AC7SOFTWARETYR B:42binding site for residue MPD B 203

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:16
2A:15 -A:74
3A:43 -A:106
4A:47 -A:108
5A:73 -B:73
6B:6 -B:16
7B:15 -B:74
8B:43 -B:106
9B:47 -B:108

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:34 -Pro A:35
2Ala B:34 -Pro B:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JI1)

(-) Exons   (0, 0)

(no "Exon" information available for 5JI1)

(-) 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:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee..eeehhhhh...eee..eee..eee..............eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5ji1 A   1 DFGLDCDEHSTESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGECEFVNPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS 109
                                    10        20        30        40        50|       74        84        94       104     
                                                                            50|                                            
                                                                             65                                            

Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee..eeehhhhh...eee..eee..eee............eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5ji1 B   1 DFGLDCDEHSTESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGECEPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS 109
                                    10        20        30        40       |67        77        87        97       107  
                                                                          48|                                           
                                                                           66                                           

   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 5JI1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JI1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JI1)

(-) Gene Ontology  (43, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:34 - Pro A:35   [ RasMol ]  
    Ala B:34 - Pro B:35   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GDF8_MOUSE | O086893hh2 3sek

(-) Related Entries Specified in the PDB File

5jhw