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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMODOMAIN OF RHINO WITH H3K9ME3
 
Authors :  S. Li, D. J. Patel
Date :  10 Jul 14  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,P,Q,R,T,U,V
Biol. Unit 1:  A,B,P,Q  (1x)
Biol. Unit 2:  C,D,R,T  (1x)
Biol. Unit 3:  E,F,U,V  (1x)
Keywords :  Pirna Biogensis, Histone Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Le Thomas, E. Stuwe, S. Li, J. Du, G. Marinov, N. Rozhkov, Y. C. Chen, Y. Luo, R. Sachidanandam, K. F. Toth, D. Patel, A. A. Aravin
Transgenerationally Inherited Pirnas Trigger Pirna Biogenesis By Changing The Chromatin Of Pirna Clusters And Inducing Precursor Processing.
Genes Dev. V. 28 1667 2014
PubMed-ID: 25085419  |  Reference-DOI: 10.1101/GAD.245514.114

(-) Compounds

Molecule 1 - RE36324P
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETSUMO
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHI, RHINO, CG10683, DMEL_CG10683
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: RHINO
 
Molecule 2 - H3(1-15)K9ME3 PEPTIDE
    Chains: P, Q, R, T, V, U
    Engineered: YES
    Other Details: PEPTIDE WAS SYNTHESIZED AT TUFTS UNIVERSITY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFPQRTUV
Biological Unit 1 (1x): AB    PQ    
Biological Unit 2 (1x):   CD    RT  
Biological Unit 3 (1x):     EF    UV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1M3L6Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 4QUF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QUF)

(-) 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:57
                                                                                        
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeee...hhhhheeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  4quf A 22 EEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRL 78
                                    31        41        51        61        71       


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  4quf B 22 EEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLHRKAAA 84
                                    31        41        51        61        71        81   


Chain C from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeee...hhhhheeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  4quf C 22 EEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLHRKA 82
                                    31        41        51        61        71        81 


Chain D from PDB  Type:PROTEIN  Length:58
                                                                                         
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  4quf D 22 EEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLH 79
                                    31        41        51        61        71        


Chain E from PDB  Type:PROTEIN  Length:58
                                                                                         
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  4quf E 22 EEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLH 79
                                    31        41        51        61        71        


Chain F from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeee...hhhhheeee.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  4quf F 23 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLHRKA 82
                                    32        42        52        62        72        82


Chain P from PDB  Type:PROTEIN  Length:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...ee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  4quf P  3 TKQTARkS 10
                                  | 
                                  9-M3L


Chain Q from PDB  Type:PROTEIN  Length:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...eee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  4quf Q  3 TKQTARkS 10
                                  | 
                                  9-M3L


Chain R from PDB  Type:PROTEIN  Length:9
                                        
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...ee.... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                  4quf R  3 TKQTARkST 11
                                  |  
                                  9-M3L


Chain T from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..eee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  4quf T  4 KQTARkS 10
                                 | 
                                 9-M3L


Chain U from PDB  Type:PROTEIN  Length:5
                                    
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                  4quf U  5 QTARk  9
                                |
                                9-M3L


Chain V from PDB  Type:PROTEIN  Length:6
                                     
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                  4quf V  5 QTARkS 10
                                | 
                                | 
                                9-M3L
   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 4QUF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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4quc