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(-) Description

Title :  PRO-BONE MORPHOGENETIC PROTEIN 9
 
Authors :  L. -Z. Mi, C. T. Brown, Y. Gao, Y. Tian, V. Le, T. Walz, T. A. Springer
Date :  20 Feb 15  (Deposition) - 04 Mar 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pro-Bmp Complex, Morphogen, Transforming Growth Factor-Beta Family, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Z. Mi, C. T. Brown, Y. Gao, Y. Tian, V. Q. Le, T. Walz, T. A. Springer
Structure Of Bone Morphogenetic Protein 9 Procomplex.
Proc. Natl. Acad. Sci. Usa V. 112 3710 2015
PubMed-ID: 25751889  |  Reference-DOI: 10.1073/PNAS.1501303112

(-) Compounds

Molecule 1 - BONE MORPHOGENETIC PROTEIN 9 GROWTH FACTOR DOMAIN
    ChainsA, B
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System OrganOVARY
    Expression System Taxid10029
    GeneGDF2, BMP9
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPRO-BMP9 PRODOMAIN,GDF-2,BONE MORPHOGENETIC PROTEIN 9,BMP-9
 
Molecule 2 - BONE MORPHOGENETIC PROTEIN 9 PRODOMAIN
    ChainsC, D
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Taxid10029
    GeneGDF2, BMP9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP9 GROWTH FACTOR,GDF-2,BONE MORPHOGENETIC PROTEIN 9,BMP-9

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2ZN10Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:141 , GLU A:212 , HIS D:304 , ASP D:345binding site for residue ZN A 303
02AC2SOFTWAREHIS A:119 , GLU A:120 , GLU A:244 , HOH A:405binding site for residue ZN A 304
03AC3SOFTWAREASP A:173 , HOH A:404 , ASP B:102 , HOH B:403 , HOH B:404binding site for residue ZN A 305
04AC4SOFTWAREGLU A:101 , GLU B:144 , HIS B:210binding site for residue ZN A 306
05AC5SOFTWAREGLU A:144 , HIS A:210 , GLU B:101binding site for residue ZN A 307
06AC6SOFTWAREASP B:136 , ASP B:215 , HIS D:359binding site for residue ZN B 303
07AC7SOFTWAREASP A:102 , HOH A:403 , ASP B:173 , HOH B:401binding site for residue ZN B 304
08AC8SOFTWAREHIS B:119 , GLU B:120 , GLU B:244binding site for residue ZN B 305
09AC9SOFTWAREGLU C:397binding site for residue ZN C 501
10AD1SOFTWAREHIS C:359 , HOH C:602 , HOH C:603binding site for residue ZN C 502
11AD2SOFTWAREASN A:113 , SER A:115 , MET C:387binding site for Poly-Saccharide residues NAG A 301 through NAG A 302 bound to ASN A 113
12AD3SOFTWAREASN B:113 , SER B:115binding site for Poly-Saccharide residues NAG B 301 through NAG B 302 bound to ASN B 113

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:133 -A:214
2B:133 -B:214
3C:305 -C:371
4C:334 -C:404
5C:338 -C:406
6D:305 -D:371
7D:334 -D:404
8D:338 -D:406

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:222 -Pro A:223
2Pro B:222 -Pro B:223
3Ala C:325 -Pro C:326
4Phe C:340 -Pro C:341
5Ala D:325 -Pro D:326
6Phe D:340 -Pro D:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YCG)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........eeeeee..eeeee........eeeeee........eeeeeeeeeeeeee....hhhhh..eeeeeeeeee..........eeeeeeeeee...eeeeeehhhhhhhhhh........eeeeeeee.......eee..........eeeeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycg A  62 PPQYMIDLYNRYTTDKSSTPASNIVRSFSVEDAISTAATEDFPFQKHILIFNISIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIRDEGWETLEVSSAVKRWVRADSTTNKNKLEVTVQSHRESCDTLDISVPPGSKNLPFFVVFSNDRSNGTKETRLELKEMIGHEQ 257
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      

Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh........eeeeee..eeeee........eeeeee........eeeeeeeeeeeeee....hhhhh..eeeeeeeeee..........eeeeeeeeee...eeeeeehhhhhhhhhh........eeeeeeee.......eee..........eeeeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ycg B  61 EPPQYMIDLYNRYTTDKSSTPASNIVRSFSVEDAISTAATEDFPFQKHILIFNISIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIRDEGWETLEVSSAVKRWVRADSTTNKNKLEVTVQSHRESCDTLDISVPPGSKNLPFFVVFSNDRSNGTKETRLELKEMIGHEQE 258
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        

Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....hhhh.eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eee..eeeeeeeee.....eeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ycg C 302 GSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR 407
                                   311       321       331       341       351       361       371       381       391       401      

Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....hhhh.eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eee..eeeeeeeee.....eeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ycg D 302 GSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR 407
                                   311       321       331       341       351       361       371       381       391       401      

   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 4YCG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (46, 84)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala C:325 - Pro C:326   [ RasMol ]  
    Ala D:325 - Pro D:326   [ RasMol ]  
    Phe C:340 - Pro C:341   [ RasMol ]  
    Phe D:340 - Pro D:341   [ RasMol ]  
    Pro A:222 - Pro A:223   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        GDF2_HUMAN | Q9UK051zkz 4fao 4mpl 4yci 5hzw 5i05
        GDF2_MOUSE | Q9WV564yci

(-) Related Entries Specified in the PDB File

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