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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTIDE TRIMETHYLATED AT LYS9
 
Authors :  E. S. Pilka, S. S. Ng, K. L. Kavanagh, M. A. Mcdonough, P. Savitsky, F. Von C. H. Arrowsmith, J. Weigelt, A. Edwards, M. Sundstrom, C. J. Schofiel U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  31 Jan 07  (Deposition) - 13 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Double-Stranded Beta Helix, Demethylase, Oxygenase, Sgc, Structural Genomics, Structural Genomics Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Ng, K. L. Kavanagh, M. A. Mcdonough, D. Butler, E. S. Pilka, B. M. Lienard, J. E. Bray, P. Savitsky, O. Gileadi, F. Von Delft, N. R. Rose, J. Offer, J. C. Scheinost, T. Borowski, M. Sundstrom, C. J. Schofield, U. Oppermann
Crystal Structures Of Histone Demethylase Jmjd2A Reveal Basis For Substrate Specificity.
Nature V. 448 87 2007
PubMed-ID: 17589501  |  Reference-DOI: 10.1038/NATURE05971

(-) Compounds

Molecule 1 - JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneJMJD2A, JHDM3A, JMJD2, KIAA0677
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJUMONJI DOMAIN-CONTAINING PROTEIN 2A
 
Molecule 2 - SYNTHETIC PEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3NI2Ligand/IonNICKEL (II) ION
4OGA2Ligand/IonN-OXALYLGLYCINE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3NI-1Ligand/IonNICKEL (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3NI-1Ligand/IonNICKEL (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , OGA A:600 , HOH A:763BINDING SITE FOR RESIDUE NI A 501
2AC2SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , OGA B:600 , HOH B:756BINDING SITE FOR RESIDUE NI B 501
4AC4SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308BINDING SITE FOR RESIDUE ZN B 502
5AC5SOFTWARETYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , LYS A:206 , HIS A:276 , SER A:288 , NI A:501 , HOH A:763 , M3L C:9 , HOH C:41BINDING SITE FOR RESIDUE OGA A 600
6AC6SOFTWARETYR B:132 , PHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , LYS B:206 , TRP B:208 , HIS B:276 , SER B:288 , NI B:501 , HOH B:756 , M3L D:9 , HOH D:75BINDING SITE FOR RESIDUE OGA B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OQ6)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJNPS51183 JmjN domain profile.KDM4A_HUMAN14-56
 
  2A:14-56
B:14-56
2HISTONE_H3_1PS00322 Histone H3 signature 1.H31_HUMAN15-21
 
  2C:14-14
D:14-14
3JMJCPS51184 JmjC domain profile.KDM4A_HUMAN142-308
 
  2A:142-308
B:142-308
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJNPS51183 JmjN domain profile.KDM4A_HUMAN14-56
 
  1A:14-56
-
2HISTONE_H3_1PS00322 Histone H3 signature 1.H31_HUMAN15-21
 
  1C:14-14
-
3JMJCPS51184 JmjC domain profile.KDM4A_HUMAN142-308
 
  1A:142-308
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJNPS51183 JmjN domain profile.KDM4A_HUMAN14-56
 
  1-
B:14-56
2HISTONE_H3_1PS00322 Histone H3 signature 1.H31_HUMAN15-21
 
  1-
D:14-14
3JMJCPS51184 JmjC domain profile.KDM4A_HUMAN142-308
 
  1-
B:142-308

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003593032bENSE00001974165chr6:27858570-27858160411H31_HUMAN1-1361362C:7-14
D:7-14
8
8

2.1bENST000003723961bENSE00001894244chr1:44115829-4411592395KDM4A_HUMAN-00--
2.3aENST000003723963aENSE00002186574chr1:44118808-44118984177KDM4A_HUMAN1-46462A:8-46
B:7-46
39
40
2.5ENST000003723965ENSE00001143140chr1:44121262-44121437176KDM4A_HUMAN47-105592A:47-105
B:47-105
59
59
2.6ENST000003723966ENSE00000957378chr1:44125969-44126083115KDM4A_HUMAN105-143392A:105-143
B:105-143
39
39
2.7ENST000003723967ENSE00000957379chr1:44128565-44128758194KDM4A_HUMAN144-208652A:144-208
B:144-208
65
65
2.8ENST000003723968ENSE00000957380chr1:44131367-4413141650KDM4A_HUMAN208-225182A:208-225
B:208-225
18
18
2.9bENST000003723969bENSE00001690958chr1:44132123-44132226104KDM4A_HUMAN225-259352A:225-259
B:225-259
35
35
2.10cENST0000037239610cENSE00000957382chr1:44132625-44132762138KDM4A_HUMAN260-305462A:260-305
B:260-305
46
46
2.11ENST0000037239611ENSE00000957383chr1:44133443-44133690248KDM4A_HUMAN306-388832A:306-355
B:306-354
50
49
2.12ENST0000037239612ENSE00000957384chr1:44134771-44134970200KDM4A_HUMAN388-455680--
2.13bENST0000037239613bENSE00000957385chr1:44137176-44137546371KDM4A_HUMAN455-5781240--
2.14ENST0000037239614ENSE00001080538chr1:44149355-44149475121KDM4A_HUMAN579-619410--
2.15ENST0000037239615ENSE00000957387chr1:44154585-44154766182KDM4A_HUMAN619-679610--
2.16bENST0000037239616bENSE00001143055chr1:44156516-44156720205KDM4A_HUMAN680-748690--
2.17ENST0000037239617ENSE00001143047chr1:44157167-4415724377KDM4A_HUMAN748-773260--
2.18bENST0000037239618bENSE00001143039chr1:44157927-4415798256KDM4A_HUMAN774-792190--
2.19ENST0000037239619ENSE00001143030chr1:44159665-44159773109KDM4A_HUMAN792-828370--
2.20ENST0000037239620ENSE00001143023chr1:44160380-44160565186KDM4A_HUMAN829-890620--
2.21ENST0000037239621ENSE00001080535chr1:44163514-44163684171KDM4A_HUMAN891-947570--
2.22aENST0000037239622aENSE00001080539chr1:44169288-44169407120KDM4A_HUMAN948-987400--
2.23ENST0000037239623ENSE00001080536chr1:44169691-4416978393KDM4A_HUMAN988-1018310--
2.24aENST0000037239624aENSE00001841454chr1:44169901-441711861286KDM4A_HUMAN1019-1064460--

(-) 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:348
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:348
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347        
          KDM4A_HUMAN     8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------JMJN  PDB: A:14-56 UniProt: 14-56          -------------------------------------------------------------------------------------JMJC  PDB: A:142-308 UniProt: 142-308                                                                                                                                  ----------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a  PDB: A:8-46 UniProt: 1-46   Exon 2.5  PDB: A:47-105 UniProt: 47-105                    --------------------------------------Exon 2.7  PDB: A:144-208 UniProt: 144-208                        ----------------Exon 2.9b  PDB: A:225-259          Exon 2.10c  PDB: A:260-305 UniProt: 260-305   Exon 2.11  PDB: A:306-355 UniProt: 306-388         Transcript 2 (1)
           Transcript 2 (2) -------------------------------------------------------------------------------------------------Exon 2.6  PDB: A:105-143               ----------------------------------------------------------------Exon 2.8          ---------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                 2oq6 A   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK 355
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347        

Chain B from PDB  Type:PROTEIN  Length:348
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:348
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        
          KDM4A_HUMAN     7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------JmjN-2oq6B03 B:15-49               -----------------------------------------------------------------------------------------------------------------------------JmjC-2oq6B01 B:175-291                                                                                               --------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------JmjN-2oq6B04 B:15-49               -----------------------------------------------------------------------------------------------------------------------------JmjC-2oq6B02 B:175-291                                                                                               --------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------JMJN  PDB: B:14-56 UniProt: 14-56          -------------------------------------------------------------------------------------JMJC  PDB: B:142-308 UniProt: 142-308                                                                                                                                  ---------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a  PDB: B:7-46 UniProt: 1-46    Exon 2.5  PDB: B:47-105 UniProt: 47-105                    --------------------------------------Exon 2.7  PDB: B:144-208 UniProt: 144-208                        ----------------Exon 2.9b  PDB: B:225-259          Exon 2.10c  PDB: B:260-305 UniProt: 260-305   Exon 2.11  PDB: B:306-354 UniProt: 306-388        Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------------Exon 2.6  PDB: B:105-143               ----------------------------------------------------------------Exon 2.8          --------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                 2oq6 B   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_HUMAN     8 ARKSTGGK  15
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                PROSITE (2) -------H PROSITE (2)
               Transcript 1 1.2b     Transcript 1
                 2oq6 C   7 ARkSTGGk  14
                              |    |
                              |    |
                              9-M3L|
                                  14-ALY

Chain D from PDB  Type:PROTEIN  Length:8
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_HUMAN     8 ARKSTGGK  15
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                PROSITE (2) -------H PROSITE (2)
               Transcript 1 1.2b     Transcript 1
                 2oq6 D   7 ARkSTGGk  14
                              |    |
                              |    |
                              9-M3L|
                                  14-ALY

   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 2OQ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OQ6)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Family: JmjC (39)
1aJmjC-2oq6B01B:175-291
1bJmjC-2oq6B02B:175-291

(-) Gene Ontology  (50, 53)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDM4A_HUMAN | O75164)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0051864    histone demethylase activity (H3-K36 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0014898    cardiac muscle hypertrophy in response to stress    The physiological enlargement or overgrowth of all or part of the heart muscle due to an increase in size (not length) of individual cardiac muscle fibers, without cell division, as a result of a disturbance in organismal or cellular homeostasis.
    GO:0070544    histone H3-K36 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
    GO:0016577    histone demethylation    The modification of histones by removal of methyl groups.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1900113    negative regulation of histone H3-K9 trimethylation    Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.

Chain C,D   (H31_HUMAN | P68431)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0060968    regulation of gene silencing    Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        KDM4A_HUMAN | O751642gf7 2gfa 2gp3 2gp5 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6x 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvr 5tvs

(-) Related Entries Specified in the PDB File

2oq7 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH NI AND N- OXALYLGLYCINE
2os2 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTIDE TRIMETHYLATED AT LYS36
2ot7 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTIDE MONOMETHYLATED AT LYS9
2ox0 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTIDE DIMETHYLATED AT LYS9