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(-) Description

Title :  CRYSTAL STRUCTURE OF SMAD5-MH1 IN COMPLEX WITH A COMPOSITE DNA SEQUENCE
 
Authors :  N. Chai, J. Wang, Z. X. Wang, J. W. Wu
Date :  22 Feb 17  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Smad5 Mh1 Domain, Composite Dna, Sbe Dna, Gc-Rich Dna, Metal Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Chai, W. X. Li, J. Wang, Z. X. Wang, S. M. Yang, J. W. Wu
Structural Basis For The Smad5 Mh1 Domain To Recognize Different Dna Sequences.
Nucleic Acids Res. V. 43 9051 2015
PubMed-ID: 26304548  |  Reference-DOI: 10.1093/NAR/GKV848

(-) Compounds

Molecule 1 - MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5
    Chains: B, A, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MH1 DOMAIN (UNP RESIDUES 1-143)
    Gene: SMAD5, MADH5, MSMAD5
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MOTHERS AGAINST DPP HOMOLOG 5,DWARFIN-C,DWF-C,SMAD FAMILY MEMBER 5,MSMAD5
 
Molecule 2 - DNA (5'- D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A) -3')
    Chains: C, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A) -3')
    Chains: D, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:65 , CYS B:110 , CYS B:122 , HIS B:127binding site for residue ZN B 201
2AC2SOFTWARECYS A:65 , CYS A:110 , CYS A:122 , HIS A:127binding site for residue ZN A 201
3AC3SOFTWARECYS E:65 , CYS E:110 , CYS E:122 , HIS E:127binding site for residue ZN E 201
4AC4SOFTWARECYS F:65 , CYS F:110 , CYS F:122 , HIS F:127binding site for residue ZN F 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X6M)

(-) Exons   (0, 0)

(no "Exon" information available for 5X6M)

(-) 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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee......eee..eeehhhhhhhhhhh.........eee.............eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6m A  12 SPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVES 133
                                    21        31        41        51        61        71        81        91       101       111       121       131  


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........ee.......eee..eeehhhhhhhhhhh.....hhh.eee..............ee.....eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6m B  13 PAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVESP 134
                                    22        32        42        52        62        72        82        92       102       112       122       132  


Chain C from PDB  Type:DNA  Length:22
                                                      
                 5x6m C   1 ATCAGACTGCCGGCAGTCTATA  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 5x6m D   1 TTATAGACTGCCGGCAGTCTGA  22
                                    10        20  


Chain E from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh........eee......eee..eeehhhhhhhhhhh.....hhh.eee......hhhhh..eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6m E  13 PAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVES 133
                                    22        32        42        52        62        72        82        92       102       112       122       132 


Chain F from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eee......eee..eeehhhhhhhhhhh.....hhh.eee......hhhhh..eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6m F  13 PAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVES 133
                                    22        32        42        52        62        72        82        92       102       112       122       132 


Chain G from PDB  Type:DNA  Length:22
                                                      
                 5x6m G   1 ATCAGACTGCCGGCAGTCTATA  22
                                    10        20  


Chain H from PDB  Type:DNA  Length:22
                                                      
                 5x6m H   1 TTATAGACTGCCGGCAGTCTGA  22
                                    10        20
   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 5X6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X6M)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  5x6m
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  SMAD5_MOUSE | P97454
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 Related Entries

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

UniProtKB/Swiss-Prot
        SMAD5_MOUSE | P97454: 5x6g 5x6h

(-) Related Entries Specified in the PDB File

5x6g 5x6h