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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RGMB-BMP2 COMPLEX, CRYSTAL FORM 1
 
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 :  2.85
Chains :  Asym./Biol. Unit :  A,B
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 - RGM DOMAIN FAMILY MEMBER B
    Chains: B
    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 52-137
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE, DRAGON, REPULSIVE GUIDANCE MOLECULE B, RGMB
 
Molecule 2 - BONE MORPHOGENETIC PROTEIN 2
    Chains: A
    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, BMP2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:82 , ARG B:86 , ASN B:120 , CYS B:121BINDING SITE FOR RESIDUE SO4 B1123
2AC2SOFTWARESER A:294 , SER A:295 , LYS A:297BINDING SITE FOR RESIDUE SO4 A1397
3AC3SOFTWAREASN A:350 , SER A:354 , LYS A:358BINDING SITE FOR RESIDUE SO4 A1398
4AC4SOFTWARELYS A:383 , GLN B:53 , CYS B:54 , ASN B:102BINDING SITE FOR RESIDUE SO4 B1124
5AC5SOFTWAREASN A:341 , ASN A:384 , TYR A:385 , GLN A:386BINDING SITE FOR RESIDUE SO4 A1399
6AC6SOFTWAREHIS A:321BINDING SITE FOR RESIDUE SO4 A1400
7AC7SOFTWAREARG A:298BINDING SITE FOR RESIDUE SO4 A1401
8AC8SOFTWARESER A:294BINDING SITE FOR RESIDUE SO4 A1402

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:296 -A:361
2A:325 -A:393
3A:329 -A:395
4B:54 -B:99
5B:59 -B:91
6B:82 -B:121

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:316 -Pro A:317
2Phe A:331 -Pro A:332
3Leu B:70 -Asn B:71
4Asn B:71 -Ser B:72
5Ser B:72 -Ala B:73
6Val B:74 -Asp B:75
7Asp B:75 -Gly B:76
8Gln B:118 -Arg B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UHZ)

(-) 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..eeehhhhh....eee..eee..eee.............hhhhhhhhhhhhhh.......eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4uhz A 293 KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR 396
                                   302       312       322       332       342       352       362       372       382       392    


Chain B from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4uhz B  53 QCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCS 122
                                    62        72        82        92       102       112       122
   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 4UHZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (117, 119)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:316 - Pro A:317   [ RasMol ]  
    Asn B:71 - Ser B:72   [ RasMol ]  
    Asp B:75 - Gly B:76   [ RasMol ]  
    Gln B:118 - Arg B:119   [ RasMol ]  
    Leu B:70 - Asn B:71   [ RasMol ]  
    Phe A:331 - Pro A:332   [ RasMol ]  
    Ser B:72 - Ala B:73   [ RasMol ]  
    Val B:74 - Asp B:75   [ RasMol ]  
 

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  4uhz
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  RGMB_HUMAN | Q6NW40
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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 4uhy 4ui0 4ui1 4ui2
        RGMB_HUMAN | Q6NW40: 4bq6 4bq7 4bq8 4ui0 4ui2

(-) Related Entries Specified in the PDB File

4uhy CRYSTAL STRUCTURE OF THE HUMAN RGMA-BMP2 COMPLEX
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