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(-) Description

Title :  CRYSTAL STRUCTURE OF NSD3 TANDEM PHD5-C5HCH DOMAINS
 
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 :  2.27
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Zinc Finger, Transcription, Histone, Nuclear Protein, Transferase (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
    Chains: A, C
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1310-1413
    Gene: WHSC1L1, NSD3, DC28
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR 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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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
5AC5SOFTWARECYS C:1324 , CYS C:1327 , HIS C:1346 , CYS C:1349BINDING SITE FOR RESIDUE ZN C 1501
6AC6SOFTWARECYS C:1336 , CYS C:1341 , CYS C:1362 , HIS C:1365BINDING SITE FOR RESIDUE ZN C 1502
7AC7SOFTWARECYS C:1378 , CYS C:1381 , CYS C:1405 , HIS C:1408BINDING SITE FOR RESIDUE ZN C 1503
8AC8SOFTWARECYS C:1367 , CYS C:1370 , CYS C:1386 , HIS C:1389BINDING SITE FOR RESIDUE ZN C 1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4GND)

(-) 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:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee........ee.hhhhh..........hhhhh.........ee......eehhhhh....ee......ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                4gnd A 1316 PKQMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1325      1335      1345      1355      1365      1375      1385      1395      1405        


Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee........ee.hhhhh..........hhhhh.........ee......ee.........ee......ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                4gnd C 1307 SNARKIKTEPKQMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1316      1326      1336      1346      1356      1366      1376      1386      1396      1406
   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 4GND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NSD3_HUMAN | Q9BZ95: 2daq 2ncz 2nd1 4gne 4gnf 4gng 4rxj 5upd

(-) Related Entries Specified in the PDB File

4gne 4gnf 4gng