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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY RGMB-BMP2-NEO1 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 :  3.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Repulsive Guidance Molecule, Bone Morphogenetic Protein Pathway, Hemojuvelin, Morphogen, Axon Guidance, Cell Surface Receptor Signaling, Neogenin, Signaling Protein (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 - NEOGENIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: 5TH AND 6TH FN TYPE 3 LIKE DOMAINS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHAIN C AND CHAIN D IS THE RESULT OF AN AUTOCATALYTIC CLEAVAGE BETWEEN RESIDUES ASP168 AND PRO169
 
Molecule 2 - BONE MORPHOGENETIC PROTEIN 2, BMP2
    Chains: 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
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
    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: RESIDUES 50-168
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: RESIDUES 169-240
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SRT3Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BMA2Ligand/IonBETA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SRT6Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:298 , HIS B:299 , PRO B:300 , PHE B:323BINDING SITE FOR RESIDUE SRT B1397
2AC2SOFTWAREHIS B:321 , HIS D:267 , GLY D:286BINDING SITE FOR RESIDUE SRT B1398
3AC3SOFTWAREASN B:341 , LYS B:383 , ASN B:384 , GLN B:386 , GLY C:101 , ASN C:102BINDING SITE FOR RESIDUE SRT B1399
4AC4SOFTWARESER B:370 , PHE D:281 , ARG D:283BINDING SITE FOR RESIDUE ACT B1400
5AC5SOFTWARETYR A:921 , ASN A:940 , GLY D:207 , SER D:208BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A2084 THROUGH BMA A2086 BOUND TO ASN A 940

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1B:296 -B:361
2B:325 -B:393
3B:329 -B:395
4C:54 -C:99
5C:59 -C:91
6C:82 -C:121
7C:139 -D:226
8C:163 -D:312
9D:181 -D:316

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1His A:913 -Gln A:914
2Ile A:930 -Pro A:931
3Ala B:316 -Pro B:317
4Leu B:337 -Asn B:338
5Gln C:118 -Arg C:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UI2)

(-) Exons   (0, 0)

(no "Exon" information available for 4UI2)

(-) 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:201
                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..eeeeeee..............eeeeeee.........eeeee...eeee.......eeeeeeeeee..ee......eeee..........eeeeeee.......eeeeee........eeeeeeeee.....hhhhheeeeee....eeee.......eeeeeeeeee..eeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ui2 A  883 TPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTP 1083
                                   892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082 


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..............eee..eee.....hhhhhh..hhhhhhhhhhhhhh.......eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                4ui2 B  293 KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR  396
                                   302       312       322       332       342       352       362       372       382       392    


Chain C from PDB  Type:PROTEIN  Length:80
                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                4ui2 C   52 AQCRIQKCTTDFVSLTSHDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSDPCNYHPSYLFCGLFGD  168
                                    61       |79        89        99       109       119  ||   158       168
                                            69|                                         122|  142|          
                                             78                                          137   158          


Chain D from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee....eeeeeee...eeeeeeeee.......eeeeeeeeee.........eeeeee.............ee.......eeeeee....eeeeee.hhheeeeeeee..eeeeeeeeehhhhh........hhhhhh.hhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ui2 D  169 PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHGCTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDD  324
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318
   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 4UI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UI2)

(-) Gene Ontology  (131, 140)

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  Cis Peptide Bonds
    Ala B:316 - Pro B:317   [ RasMol ]  
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    His A:913 - Gln A:914   [ RasMol ]  
    Ile A:930 - Pro A:931   [ RasMol ]  
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  4ui2
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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 4ui0 4ui1
        NEO1_MOUSE | P97798: 4bq6 4bq7 4bq8 4bq9 4bqb 4bqc 4pln
        RGMB_HUMAN | Q6NW40: 4bq6 4bq7 4bq8 4uhz 4ui0

(-) 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
4ui0 CRYSTAL STRUCTURE OF THE HUMAN RGMB-BMP2 COMPLEX, CRYSTAL FORM 2
4ui1 CRYSTAL STRUCTURE OF THE HUMAN RGMC-BMP2 COMPLEX