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(-) Description

Title :  CRYSTAL STRUCTURE OF NSD3 TANDEM PHD5-C5HCH DOMAINS COMPLEXED WITH H3 PEPTIDE 1-15
 
Authors :  F. Li, C. He, J. Wu, Y. Shi
Date :  17 Aug 12  (Deposition) - 02 Jan 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Zinc Finger, Transcription, Histone, Nuclear Protein, Transferase- Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. He, F. Li, J. Zhang, J. Wu, Y. Shi
The Methyltransferase Nsd3 Has Chromatin-Binding Motifs, Phd5-C5Hch, That Are Distinct From Other Nsd (Nuclear Receptor Set Domain) Family Members In Their Histone H3 Recognition.
J. Biol. Chem. V. 288 4692 2013
PubMed-ID: 23269674  |  Reference-DOI: 10.1074/JBC.M112.426148

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE NSD3
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1310-1413
    GeneWHSC1L1, NSD3, DC28
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR SET DOMAIN-CONTAINING PROTEIN 3, PROTEIN WHISTLE, WHSC1-LIKE 1 ISOFORM 9 WITH METHYLTRANSFERASE ACTIVITY TO LYSINE, WOLF-HIRSCHHORN SYNDROME CANDIDATE 1-LIKE PROTEIN 1, WHSC1-LIKE PROTEIN 1
 
Molecule 2 - HISTONE H3.3
    ChainsC
    EngineeredYES
    FragmentUNP RESIDUES 2-16
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

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 A:1324 , CYS A:1327 , HIS A:1346 , CYS A:1349BINDING SITE FOR RESIDUE ZN A 1501
2AC2SOFTWARECYS A:1336 , CYS A:1341 , CYS A:1362 , HIS A:1365BINDING SITE FOR RESIDUE ZN A 1502
3AC3SOFTWARECYS A:1378 , CYS A:1381 , CYS A:1405 , HIS A:1408BINDING SITE FOR RESIDUE ZN A 1503
4AC4SOFTWARECYS A:1367 , CYS A:1370 , CYS A:1386 , HIS A:1389BINDING SITE FOR RESIDUE ZN A 1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GNF)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:96
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeee........ee.hhhhh..........hhhhh.........ee......ee.........ee......ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                4gnf A 1318 QMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1327      1337      1347      1357      1367      1377      1387      1397      1407      

Chain C from PDB  Type:PROTEIN  Length:9
                                          
               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
                4gnf C    1 ARTKQTARK    9

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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 4GNF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H33_HUMAN | P842431pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x
        NSD3_HUMAN | Q9BZ952daq 2ncz 2nd1 4gnd 4gne 4gng 4rxj 5upd

(-) Related Entries Specified in the PDB File

4gnd 4gne 4gng