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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RGMA-BMP2 COMPLEX
 
Authors :  E. G. Healey, B. Bishop, J. Elegheert, C. H. Bell, S. Padilla-Parra, C. S
Date :  27 Mar 15  (Deposition) - 06 May 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Signaling Protein, Bone Morphogenetic Protein Pathway, Hemojuvelin, Morphogen, Axon Guidance, Cell Surface Receptor Signaling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. G. Healey, B. Bishop, J. Elegheert, C. H. Bell, S. Padilla-Parra, C. Siebold
Repulsive Guidance Molecule Is A Structural Bridge Between Neogenin And Bone Morphogenetic Protein.
Nat. Struct. Mol. Biol. V. 22 458 2015
PubMed-ID: 25938661  |  Reference-DOI: 10.1038/NSMB.3016

(-) Compounds

Molecule 1 - REPULSIVE GUIDANCE MOLECULE A
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: N-TERMINAL DOMAIN, RESIDUES 45-140
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RGM DOMAIN FAMILY MEMBER A, RGMA
 
Molecule 2 - BONE MORPHOGENETIC PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PET22B
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BMP-2, BONE MORPHOGENETIC PROTEIN 2A, BMP-2A, BONE MORPHOGENETIC PROTEIN 2, BMP2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4UHY)

(-) Sites  (0, 0)

(no "Site" information available for 4UHY)

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:296 -A:361
2A:325 -A:393
3A:329 -A:395
4A:360 -B:360
5B:296 -B:361
6B:325 -B:393
7B:329 -B:395
8C:48 -C:93
9C:53 -C:85
10C:76 -C:115

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ala A:316 -Pro A:317
2Phe A:331 -Pro A:332
3Ala B:316 -Pro B:317
4Phe B:331 -Pro B:332
5Thr C:61 -Ser C:62
6Ser C:62 -Gly C:63
7Gly C:63 -Ser C:64
8Asp C:71 -Thr C:72
9Pro C:73 -Glu C:74
10Phe C:75 -Cys C:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UHY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UHY)

(-) Exons   (0, 0)

(no "Exon" information available for 4UHY)

(-) 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:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....hhhh.eee..eee..eee.............hhhhhhhhhhhh.........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4uhy A 293 KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR 396
                                   302       312       322       332       342       352       362       372       382       392    


Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee....hhhh.eee..eee..eee.............hhhhhhhhhhhh.........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4uhy B 292 LKSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR 396
                                   301       311       321       331       341       351       361       371       381       391     


Chain C from PDB  Type:PROTEIN  Length:64
                                                                                                
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 4uhy C  47 PCKILKCNSEFWSATSGSDTPEFCAALRSYALCTRRTARTCRGDLAYHSAVHGIEDLMSQHNCS 116
                                    56       |72        82        92       102       112    
                                            64|                                             
                                             71
   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 4UHY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UHY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UHY)

(-) Gene Ontology  (114, 117)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4uhy)
 
  Cis Peptide Bonds
    Ala A:316 - Pro A:317   [ RasMol ]  
    Ala B:316 - Pro B:317   [ RasMol ]  
    Asp C:71 - Thr C:72   [ RasMol ]  
    Gly C:63 - Ser C:64   [ RasMol ]  
    Phe A:331 - Pro A:332   [ RasMol ]  
    Phe B:331 - Pro B:332   [ RasMol ]  
    Phe C:75 - Cys C:76   [ RasMol ]  
    Pro C:73 - Glu C:74   [ RasMol ]  
    Ser C:62 - Gly C:63   [ RasMol ]  
    Thr C:61 - Ser C:62   [ RasMol ]  
 

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  BMP2_HUMAN | P12643
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  RGMA_HUMAN | Q96B86
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 Related Entries

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

UniProtKB/Swiss-Prot
        BMP2_HUMAN | P12643: 1es7 1reu 1rew 2goo 2h62 2h64 2qj9 2qja 2qjb 3bk3 3bmp 4mid 4n1d 4uhz 4ui0 4ui1 4ui2

(-) Related Entries Specified in the PDB File

4uhz CRYSTAL STRUCTURE OF THE HUMAN RGMB-BMP2 COMPLEX, CRYSTAL FORM 1
4ui0 CRYSTAL STRUCTURE OF THE HUMAN RGMB-BMP2 COMPLEX, CRYSTAL FORM 2
4ui1 CRYSTAL STRUCTURE OF THE HUMAN RGMC-BMP2 COMPLEX
4ui2 CRYSTAL STRUCTURE OF THE TERNARY RGMB-BMP2-NEO1 COMPLEX