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(-) Description

Title :  STRUCTURE OF THE GREM2-GDF5 INHIBITORY COMPLEX
 
Authors :  K. Nolan, T. B. Thompson, R. J. Read
Date :  13 Jan 16  (Deposition) - 24 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A (1x),C (1x),E (1x),F (1x)
Biol. Unit 2:  A (1x),C (1x),E (1x),F (1x)
Biol. Unit 3:  B (1x),D (1x),G (1x),H (1x)
Biol. Unit 4:  B (1x),D (1x),G (1x),H (1x)
Keywords :  Dan-Family, Bone Morphogenetic Proteins, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nolan, C. Kattamuri, S. A. Rankin, R. J. Read, A. M. Zorn, T. B. Thompson
Structure Of Gremlin-2 In Complex With Gdf5 Gives Insight Into Dan-Family-Mediated Bmp Antagonism.
Cell Rep V. 16 2077 2016
PubMed-ID: 27524626  |  Reference-DOI: 10.1016/J.CELREP.2016.07.046

(-) Compounds

Molecule 1 - GREMLIN-2
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GREM2, CKTSF1B2, PRDC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CYSTEINE KNOT SUPERFAMILY 1,BMP ANTAGONIST 2,PROTEIN RELATED TO DAN AND CERBERUS,PRDC
 
Molecule 2 - GROWTH/DIFFERENTIATION FACTOR 5
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GDF5, BMP14, CDMP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GDF-5,BONE MORPHOGENETIC PROTEIN 14,BMP-14,CARTILAGE-DERIVED MORPHOGENETIC PROTEIN 1,CDMP-1,LIPOPOLYSACCHARIDE-ASSOCIATED PROTEIN 4,LPS-ASSOCIATED PROTEIN 4,RADOTERMIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A (1x) C (1x) E (1x)F (1x)  
Biological Unit 2 (1x): A (1x) C (1x) E (1x)F (1x)  
Biological Unit 3 (1x):  B (1x) D (1x)  G (1x)H (1x)
Biological Unit 4 (1x):  B (1x) D (1x)  G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5HK5)

(-) Sites  (0, 0)

(no "Site" information available for 5HK5)

(-) SS Bonds  (30, 30)

Asymmetric Unit
No.Residues
1A:19 -A:85
2A:48 -A:117
3A:52 -A:119
4A:84 -C:84
5B:19 -B:85
6B:48 -B:117
7B:52 -B:119
8B:84 -D:84
9C:19 -C:85
10C:48 -C:117
11C:52 -C:119
12D:19 -D:85
13D:48 -D:117
14D:52 -D:119
15E:73 -E:123
16E:87 -E:137
17E:97 -E:155
18E:101 -E:157
19F:73 -F:123
20F:87 -F:137
21F:97 -F:155
22F:101 -F:157
23G:73 -G:123
24G:87 -G:137
25G:97 -G:155
26G:101 -G:157
27H:73 -H:123
28H:87 -H:137
29H:97 -H:155
30H:101 -H:157

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Asp E:141 -Pro E:142
2Asp F:141 -Pro F:142
3Pro G:138 -Gly G:139
4Asp G:141 -Pro G:142
5Pro H:138 -Gly H:139
6Asp H:141 -Pro H:142
7Ala A:39 -Pro A:40
8Phe A:54 -Pro A:55
9Ala B:39 -Pro B:40
10Phe B:54 -Pro B:55
11Ala C:39 -Pro C:40
12Phe C:54 -Pro C:55
13Ala D:39 -Pro D:40
14Phe D:54 -Pro D:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HK5)

(-) Exons   (0, 0)

(no "Exon" information available for 5HK5)

(-) 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:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeehhhhh....eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eeeeeeeeeeeeee....eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 A  16 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 120
                                    25        35        45        55        65        75        85        95       105       115     


Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeehhhhh....eee..eee..eee.............hhhhhhhhhhhhhh........eeeeeeeeeeeeee....eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 B  16 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 120
                                    25        35        45        55        65        75        85        95       105       115     


Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeehhhhh....eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 C  16 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 120
                                    25        35        45        55        65        75        85        95       105       115     


Chain D from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeehhhhh....eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 D  16 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 120
                                    25        35        45        55        65        75        85        95       105       115     


Chain E from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.......eeeee.hhh...eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 E  26 PAGAIPSPYWHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLS 163
                                    45        55        65        75        85        95       105       115       125       135       145       155        
                                   34|                                                                                                                      
                                    45                                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...........hhhhh...eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 F  26 PAGAIPSPYKWHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLS 163
                                    35|       54        64        74        84        94       104       114       124       134       144       154         
                                    35|                                                                                                                      
                                     45                                                                                                                      


Chain G from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.......eeeee.hhh...eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 G  26 PAGAIPSPYKWHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLS 163
                                    35|       54        64        74        84        94       104       114       124       134       144       154         
                                    35|                                                                                                                      
                                     45                                                                                                                      


Chain H from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhh...eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeee.............eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk5 H  45 WHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLS 163
                                    54        64        74        84        94       104       114       124       134       144       154
   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 5HK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HK5)

(-) Gene Ontology  (46, 50)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:39 - Pro A:40   [ RasMol ]  
    Ala B:39 - Pro B:40   [ RasMol ]  
    Ala C:39 - Pro C:40   [ RasMol ]  
    Ala D:39 - Pro D:40   [ RasMol ]  
    Asp E:141 - Pro E:142   [ RasMol ]  
    Asp F:141 - Pro F:142   [ RasMol ]  
    Asp G:141 - Pro G:142   [ RasMol ]  
    Asp H:141 - Pro H:142   [ RasMol ]  
    Phe A:54 - Pro A:55   [ RasMol ]  
    Phe B:54 - Pro B:55   [ RasMol ]  
    Phe C:54 - Pro C:55   [ RasMol ]  
    Phe D:54 - Pro D:55   [ RasMol ]  
    Pro G:138 - Gly G:139   [ RasMol ]  
    Pro H:138 - Gly H:139   [ RasMol ]  
 
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  GREM2_MOUSE | O88273
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 Related Entries

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

UniProtKB/Swiss-Prot
        GDF5_HUMAN | P43026: 1waq 2bhk 3evs 3qb4
        GREM2_MOUSE | O88273: 4jph

(-) Related Entries Specified in the PDB File

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