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(-) Description

Title :  CRYSTAL STRUCTURE OF SETD2 BOUND TO HISTONE H3.3 K36M PEPTIDE
 
Authors :  S. Yang, X. Zheng, H. Li
Date :  25 Apr 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Set Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yang, X. Zheng, C. Lu, G. M. Li, C. D. Allis, H. Li
Molecular Basis For Oncohistone H3 Recognition By Setd2 Methyltransferase
Genes Dev. V. 30 1611 2016
PubMed-ID: 27474439  |  Reference-DOI: 10.1101/GAD.284323.116

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD2
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1434-1711
    Gene: SETD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HIF-1,HUNTINGTIN YEAST PARTNER B,HUNTINGTIN-INTERACTING PROTEIN 1,HIP-1,HUNTINGTIN-INTERACTING PROTEIN B,LYSINE N- METHYLTRANSFERASE 3A,SET DOMAIN-CONTAINING PROTEIN 2,HSET2,P231HBP
 
Molecule 2 - HISTONE H3.3
    Chains: B
    Engineered: YES
    Fragment: H3 PEPTIDE, UNP RESIDUES 30-43
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SCN5Ligand/IonTHIOCYANATE ION
3ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1801
2AC2SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539binding site for residue ZN A 1802
3AC3SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1803
4AC4SOFTWARELYS A:1560 , GLY A:1561 , TRP A:1562 , HIS A:1603 , TYR A:1604 , TYR A:1605 , ARG A:1625 , PHE A:1626 , ASN A:1628 , HIS A:1629 , TYR A:1666 , LYS A:1677 , CYS A:1678 , PHE A:1679 , HOH A:1948 , HOH A:2000 , HOH A:2036binding site for residue SAH A 1804
5AC5SOFTWAREMET A:1497 , GLN A:1498 , CYS A:1499 , ASN A:1522 , CYS A:1529 , SER A:1530 , CYS A:1533binding site for residue SCN A 1805
6AC6SOFTWAREHIS A:1629 , PHE A:1668 , ARG A:1686 , GLY A:1690 , GLY A:1691 , HOH A:1981binding site for residue SCN A 1806
7AC7SOFTWARECYS A:1463binding site for residue SCN A 1807
8AC8SOFTWARECYS A:1539 , SER A:1540 , GLN A:1548 , HOH A:1972 , HOH A:1996binding site for residue SCN A 1808
9AC9SOFTWARETHR A:1637 , LYS A:1639 , PRO B:38 , HIS B:39 , ARG B:40 , HOH B:208binding site for residue SCN B 101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1463 -A:1807

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JJY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JJY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JJY)

(-) Exons   (0, 0)

(no "Exon" information available for 5JJY)

(-) 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
(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:247
                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh.......ee....ee.............hhhhhhh........hhhhhh.........hhhhh............eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhh......eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeee....ee.........................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jjy A 1447 PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGK 1703
                                  1456      1466      1476      1486|     1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626      1636      1646      1656      1666      1676      1686      1696       
                                                                1486|                                                                                                                                                                                                              
                                                                 1497                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:14
                                               
               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
                5jjy B   29 APSTGGVMKPHRYR   42
                                    38
   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 5JJY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JJY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JJY)

(-) Gene Ontology  (59, 63)

Asymmetric/Biological Unit(hide GO term definitions)

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  5jjy
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  H33_HUMAN | P84243
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  SETD2_HUMAN | Q9BYW2
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  2.1.1.43
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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 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 5jlb 5kdm 5x7x
        SETD2_HUMAN | Q9BYW2: 2a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jlb 5jle 5lss 5lsx 5lsy 5lsz 5lt6 5lt7 5lt8 5v21 5v22

(-) Related Entries Specified in the PDB File

5jlb 5jle