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(-) Description

Title :  CRYSTAL STRUCTURE OF NSD3 TANDEM PHD5-C5HCH DOMAINS COMPLEXED WITH H3K9ME3 PEPTIDE
 
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 :  1.73
Chains :  Asym. Unit :  A,B,D,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Zinc Finger, Transcription, Histone, Lysine Methyaltion, 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
    Chains: A, D
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1310-1413
    Gene: WHSC1L1, NSD3, DC28
    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
 
Molecule 2 - HISTONE H3.3
    Chains: B, F
    Engineered: YES
    Fragment: UNP RESIDUES 2-16
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDF
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1324 , CYS A:1327 , HIS A:1346 , CYS A:1349BINDING SITE FOR RESIDUE ZN A 1501
02AC2SOFTWARECYS A:1336 , CYS A:1341 , CYS A:1362 , HIS A:1365BINDING SITE FOR RESIDUE ZN A 1502
03AC3SOFTWARECYS A:1378 , CYS A:1381 , CYS A:1405 , HIS A:1408BINDING SITE FOR RESIDUE ZN A 1503
04AC4SOFTWARECYS A:1367 , CYS A:1370 , CYS A:1386 , HIS A:1389BINDING SITE FOR RESIDUE ZN A 1504
05AC5SOFTWARETRP A:1364 , PHE A:1377 , GLU A:1379 , HOH A:1651 , HOH A:1661BINDING SITE FOR RESIDUE GOL A 1505
06AC6SOFTWARECYS A:1327 , HIS A:1346 , CYS A:1349 , ARG B:8BINDING SITE FOR RESIDUE GOL B 101
07AC7SOFTWARETRP D:1364 , PHE D:1377 , GLU D:1379BINDING SITE FOR RESIDUE GOL B 102
08AC8SOFTWARECYS D:1324 , CYS D:1327 , HIS D:1346 , CYS D:1349BINDING SITE FOR RESIDUE ZN D 1501
09AC9SOFTWARECYS D:1336 , CYS D:1341 , CYS D:1362 , HIS D:1365BINDING SITE FOR RESIDUE ZN D 1502
10BC1SOFTWARECYS D:1378 , CYS D:1381 , CYS D:1405 , HIS D:1408BINDING SITE FOR RESIDUE ZN D 1503
11BC2SOFTWARECYS D:1367 , CYS D:1370 , CYS D:1386 , HIS D:1389BINDING SITE FOR RESIDUE ZN D 1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GNG)

(-) 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:95
                                                                                                                                
               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
                4gng A 1319 MHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1328      1338      1348      1358      1368      1378      1388      1398      1408     


Chain B from PDB  Type:PROTEIN  Length:10
                                           
               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
                4gng B    1 ARTKQTARkS   10
                                    10
                                    9-M3L


Chain D from PDB  Type:PROTEIN  Length:97
                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee........ee.hhhhh..........hhhhh.........ee......eehhhhh....ee......ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                4gng D 1317 KQMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1326      1336      1346      1356      1366      1376      1386      1396      1406       


Chain F from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4gng F    1 ARTKQTARkS   10
                                    10
                                    9-M3L
   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 4GNG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 43)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 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 | Q9BZ95: 2daq 2ncz 2nd1 4gnd 4gne 4gnf 4rxj 5upd

(-) Related Entries Specified in the PDB File

4gnd 4gne 4gnf