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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE KDM2A-H3K36ME1 WITH NOG
 
Authors :  Z. J. Cheng, D. J. Patel
Date :  20 Jul 14  (Deposition) - 05 Nov 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Cupin Subfamily Fe(Ii)/2-Og Dioxygenase, Jmjc Domain, Histone Demethylase, Oxidoreductase-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Cheng, P. Cheung, A. J. Kuo, E. T. Yukl, C. M. Wilmot, O. Gozani, D. J. Patel
A Molecular Threading Mechanism Underlies Jumonji Lysine Demethylase Kdm2A Regulation Of Methylated H3K36.
Genes Dev. V. 28 1758 2014
PubMed-ID: 25128496  |  Reference-DOI: 10.1101/GAD.246561.114

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 2A
    Chains: A, C
    EC Number: 1.14.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 36-364
    Gene: KDM2A, FBXL11, JHDM1A, KIAA1004
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11, F-BOX/LRR-REPEAT PROTEIN 11, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A
 
Molecule 2 - LYSINE-SPECIFIC DEMETHYLASE 2A
    Chains: B, D
    EC Number: 1.14.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 450-517
    Gene: KDM2A, FBXL11, JHDM1A, KIAA1004
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11, F-BOX/LRR-REPEAT PROTEIN 11, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A
 
Molecule 3 - HISTONE H3.2
    Chains: E, F
    Engineered: YES
    Fragment: UNP RESIDUES 30-44
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONO-METHYLATED H3 PEPTIDE WAS SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MLZ2Mod. Amino AcidN-METHYL-LYSINE
2NI2Ligand/IonNICKEL (II) ION
3OGA2Ligand/IonN-OXALYLGLYCINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MLZ1Mod. Amino AcidN-METHYL-LYSINE
2NI-1Ligand/IonNICKEL (II) ION
3OGA1Ligand/IonN-OXALYLGLYCINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MLZ1Mod. Amino AcidN-METHYL-LYSINE
2NI-1Ligand/IonNICKEL (II) ION
3OGA1Ligand/IonN-OXALYLGLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:142 , ILE A:144 , LEU A:201 , THR A:209 , HIS A:212 , ASP A:214 , TYR A:222 , LYS A:229 , HIS A:284 , NI A:601 , HOH A:721 , MLZ E:36BINDING SITE FOR RESIDUE OGA A 600
2AC2SOFTWAREHIS A:212 , ASP A:214 , HIS A:284 , OGA A:600 , HOH A:843BINDING SITE FOR RESIDUE NI A 601
3AC3SOFTWAREASN C:142 , ILE C:144 , THR C:209 , HIS C:212 , ASP C:214 , VAL C:220 , TYR C:222 , LYS C:229 , HIS C:284 , VAL C:286 , NI C:601 , MLZ F:36BINDING SITE FOR RESIDUE OGA C 600
4AC4SOFTWAREHIS C:212 , ASP C:214 , HIS C:284 , OGA C:600 , HOH C:817BINDING SITE FOR RESIDUE NI C 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QXH)

(-) 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:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee.....eeeeehhhhhhhhhhhhhhh...eeeeeee...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhh.......eeeee....eeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhhhh.....hhhhhh...eeeeee...eeee....eeeee....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qxh A  36 RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME 364
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355         


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4qxh B 450 QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALTGVPIVQWP 517
                                   459       469       479       489       499       509        


Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee.....eeeeehhhhhhhhhhhhhhh...eeeeeee.....hhhhh..hhhhhhhhhhhhh.hhhhhhhh.....hhhhh.......eeeee....eeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhhhh.....hhhhh....eeeeee...eeee....eeeee....eeeeeeee....hhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qxh C  36 RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME 364
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355         


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4qxh D 450 QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALTGVPIVQWP 517
                                   459       469       479       489       499       509        


Chain E from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4qxh E  29 APATGGVkKPHRY  41
                                   |38   
                                  36-MLZ 


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4qxh F  30 PATGGVkKPH  39
                                  | 39
                                 36-MLZ
   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 4QXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 58)

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 Related Entries

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

UniProtKB/Swiss-Prot
        F6YRW4_MOUSE | F6YRW4: 4qwn 4qx7 4qx8 4qxb 4qxc
        H32_MOUSE | P84228: 1kx4 1kx5 2v86 2v87 2v88 4qwn 4qx7 4qx8 4qxb 4qxc
        KDM2A_MOUSE | P59997: 4qwn 4qx7 4qx8 4qxb 4qxc 4tn7

(-) Related Entries Specified in the PDB File

4qwn 4qx7 4qx8 4qxb 4qxc 4tn7