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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RGMB-BMP2 COMPLEX, CRYSTAL FORM 2
 
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 :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Keywords :  Signaling Protein, Repulsive Guidance Molecule, 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: 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 53-136
    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, 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, BMP2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FLC1Ligand/IonCITRATE ANION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FLC1Ligand/IonCITRATE ANION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2010 , HOH A:2012 , GLY B:319 , TYR B:320 , HIS B:321 , HOH B:2003BINDING SITE FOR RESIDUE FLC A1398
2AC2SOFTWARESER A:370 , LEU A:372 , SER B:370BINDING SITE FOR RESIDUE MPD A1397

(-) SS Bonds  (10, 10)

Asymmetric 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:54 -C:99
9C:59 -C:91
10C:82 -C:121

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:316 -Pro A:317
2Ala B:316 -Pro B:317
3His B:336 -Leu B:337
4Gln C:118 -Arg C:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UI0)

(-) Exons   (0, 0)

(no "Exon" information available for 4UI0)

(-) 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:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....hhhhh.....eee..eee..........hhhhhhhhhhhh.........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4ui0 A 293 KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR 396
                                   302       312       322       332|      345       355       365       375       385       395 
                                                                 332|                                                            
                                                                  336                                                            


Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....hhhhh.....eee..eee...hhhhhh....hhhhhhhhhhhh.........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4ui0 B 293 KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR 396
                                   302       312       322       332       342       352       362       372       382       392    


Chain C from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4ui0 C  53 QCRIQKCTTDFVSLTSCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNC 121
                                    62     || 85        95       105       115      
                                          68|                                       
                                           82
   Legend:   → Mismatch (orange background)
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  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 4UI0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UI0)

(-) Gene Ontology  (117, 119)

Asymmetric Unit(hide GO term definitions)

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  4ui0
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  BMP2_HUMAN | P12643
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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 4uhz 4ui1 4ui2
        RGMB_HUMAN | Q6NW40: 4bq6 4bq7 4bq8 4uhz 4ui2

(-) Related Entries Specified in the PDB File

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