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(-) Description

Title :  CRYSTAL STRUCTURE OF SHH1 SAWADEE DOMAIN IN COMPLEX WITH H3K9ME1 PEPTIDE
 
Authors :  J. Du, D. J. Patel
Date :  21 Jan 13  (Deposition) - 01 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Tandem Tudor, Zinc Finger, H3K9Me2, 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 - SAWADEE HOMEODOMAIN HOMOLOG 1
    Chains: A, B
    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) K9ME1 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): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CVM2Ligand/IonCYMAL-4
2MLZ1Mod. Amino AcidN-METHYL-LYSINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CVM1Ligand/IonCYMAL-4
2MLZ-1Mod. Amino AcidN-METHYL-LYSINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CVM1Ligand/IonCYMAL-4
2MLZ1Mod. Amino AcidN-METHYL-LYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:191 , HIS A:225 , CYS A:230 , CYS A:232BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREPHE A:129 , PHE A:145 , VAL A:175 , LYS A:176 , VAL A:179 , THR B:147 , CVM B:302BINDING SITE FOR RESIDUE CVM A 302
3AC3SOFTWARECYS B:191 , HIS B:225 , CYS B:230 , CYS B:232BINDING SITE FOR RESIDUE ZN B 301
4AC4SOFTWARETHR A:147 , TYR A:148 , CVM A:302 , PHE B:129 , PHE B:145 , LYS B:176 , VAL B:179BINDING SITE FOR RESIDUE CVM B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IUU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IUU)

(-) 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eeeeeeeeeeee.....eeeeeee...eeeehhhheee..ee.hhhhhhhh....eeeeeee...eeeeeeeeeeee...........eeeeee.....eeeehhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iuu A 125 ADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQEREQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRPE 257
                                   134       144       154       164|      179       189       199       210       220       230       240       250       
                                                                 164|                                  207|                                                
                                                                  170                                   209                                                


Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......eeeeeeeeeeee.....eeeeeee...hhhhheeeehhhheee..ee....hhhhh....eeeeeee....eeeeeeeeeeee...........eeeeee.....eeeehhh.eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iuu B 124 SADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQEREDQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRPE 257
                                   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
                 4iuu C   3 TKQTARkS  10
                                  | 
                                  9-MLZ
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4IUU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4iur 4iut 4iuv 5hh7 5vah 5vbc
        SHH1_ARATH | Q9XI47: 4iup 4iuq 4iur 4iut 4iuv

(-) Related Entries Specified in the PDB File

4iup 4iuq 4iur 4iut 4iuv