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(-) Description

Title :  CRYSTAL STRUCTURE OF SHH1 SAWADEE DOMAIN IN COMPLEX WITH H3K9ME3 PEPTIDE
 
Authors :  D. J. Patel, J. Du
Date :  21 Jan 13  (Deposition) - 01 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Tandem Tudor, Zinc Finger, H3K9Me3, Mediate Interaction, Histone, Methylation, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Law, J. Du, C. J. Hale, S. Feng, K. Krajewski, A. M. Palanca, B. D. Strahl, D. J. Patel, S. E. Jacobsen
Polymerase Iv Occupancy At Rna-Directed Dna Methylation Sites Requires Shh1.
Nature V. 498 385 2013
PubMed-ID: 23636332  |  Reference-DOI: 10.1038/NATURE12178

(-) Compounds

Molecule 1 - SHH1 SAWADEE
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SHH1 SAWADEE DOMAIN (UNP RESIDUES 125-258)
    Gene: F9L1.16, AT1G15215, AT1G15215
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: UNCHARACTERIZED PROTEIN
 
Molecule 2 - HISTONE H3.2, H3(1-15)K9ME3
    Chains: C
    Engineered: YES
    Fragment: H3(1-15) K9ME3 PEPTIDE (UNP RESIDUES 2-16)
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x):  BC
Biological Unit 2 (1x): A  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CVM2Ligand/IonCYMAL-4
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CVM1Ligand/IonCYMAL-4
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CVM1Ligand/IonCYMAL-4
2M3L-1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:191 , HIS B:225 , CYS B:230 , CYS B:232BINDING SITE FOR RESIDUE ZN B 301
2AC2SOFTWAREPHE B:129 , PHE B:145 , VAL B:175 , LYS B:176 , VAL B:179BINDING SITE FOR RESIDUE CVM B 302
3AC3SOFTWARECYS A:191 , HIS A:225 , CYS A:230 , CYS A:232BINDING SITE FOR RESIDUE ZN A 301
4AC4SOFTWAREPHE A:145 , LYS A:176 , VAL A:179BINDING SITE FOR RESIDUE CVM A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IUR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:166 -Asn A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IUR)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eeeeeeeeeeee.....eeeeeee........eeeehhhheee..ee.hhhhhhhh....eeeeeeee..eeeeeeeeeeeee...........eeeeee.....eeeehhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iur A 125 ADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQEREDQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRPE 257
                                   134       144       154       164       174       184       194       204       214       224       234       244       254   


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......eeeeeeeeeeee.....eeeeeee...hhhhheeeehhhheee..ee.hhhhhhhh....eeeeeee....eeeeeeeeeeee...........eeeeee.....eeeehhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iur B 124 SADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQEREDQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRP 256
                                   133       143       153       163       173       183       193       203       213       223       233       243       253   


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4iur C   3 TKQTARkS  10
                                  | 
                                  9-M3L
   Legend:   → Mismatch (orange background)
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  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 4IUR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 12)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H32_ARATH | P59226: 4ft2 4ft4 4iut 4iuu 4iuv 5hh7 5vah 5vbc
        SHH1_ARATH | Q9XI47: 4iup 4iuq 4iut 4iuu 4iuv

(-) Related Entries Specified in the PDB File

4iup 4iuq 4iut 4iuu 4iuv