IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science (0036-8075) 2006 imex curation Huang Y., Fang J., Bedford MT., Zhang Y., Xu RM. Chromatin - Epigenetic interactions resulting in chromatin modulation rmxu@saturn.med.nyu.edu 23-JAN-2007: Contacted by JYOTI. orchard Only protein-protein interactions in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Huang Y., Fang J., Bedford MT., Zhang Y., Xu RM. Chromatin - Epigenetic interactions resulting in chromatin modulation rmxu@saturn.med.nyu.edu Accepted 2006-Not a month!-19 by ORCHARD. 23-JAN-2007: Contacted by JYOTI. Science (0036-8075) 2006 orchard Only protein-protein interactions imex curation Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science (0036-8075) 2006 imex curation Huang Y., Fang J., Bedford MT., Zhang Y., Xu RM. Chromatin - Epigenetic interactions resulting in chromatin modulation rmxu@saturn.med.nyu.edu 23-JAN-2007: Contacted by JYOTI. orchard Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Huang Y., Fang J., Bedford MT., Zhang Y., Xu RM. Chromatin - Epigenetic interactions resulting in chromatin modulation rmxu@saturn.med.nyu.edu Accepted 2006-Not a month!-19 by ORCHARD. 23-JAN-2007: Contacted by JYOTI. Science (0036-8075) 2006 orchard Only protein-protein interactions imex curation h3_peptide_1-10 AA 1-10 protein protein human Homo sapiens Human ARTKQTARKS An amino acid sequence which is not represented in UniProt The AA 1- 10 consensus sequence found in most histone H3 proteins. Similar to P84244 Similar to P84243 8679210DC1B6D321 kdm4a_human Lysine-specific demethylase 4A KDM4A JMJD2 KIAA0677 Jumonji domain-containing protein 2A JHDM3A [histone H3]-trimethyl-L-lysine(36) demethylase 4A [histone H3]-trimethyl-L-lysine(9) demethylase 4A JMJD2A JmjC domain-containing histone demethylation protein 3A protein protein human Homo sapiens Human MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESELPPRAGNEEECPEEDMEGVEDGEEGDLKTSLAKHRIGTKRHRVCLEIPQEVSQSELFPKEDLSSEQYEMTECPAALAPVRPTHSSVRQVEDGLTFPDYSDSTEVKFEELKNVKLEEEDEEEEQAAAALDLSVNPASVGGRLVFSGSKKKSSSSLGSGSSRDSISSDSETSEPLSCRAQGQTGVLTVHSYAKGDGRVTVGEPCTRKKGSAARSFSERELAEVADEYMFSLEENKKSKGRRQPLSKLPRHHPLVLQECVSDDETSEQLTPEEEAEETEAWAKPLSQLWQNRPPNFEAEKEFNETMAQQAPHCAVCMIFQTYHQVEFGGFNQNCGNASDLAPQKQRTKPLIPEMCFTSTGCSTDINLSTPYLEEDGTSILVSCKKCSVRVHASCYGVPPAKASEDWMCSRCSANALEEDCCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCIFCKKRRKRTAGCCVQCSHGRCPTAFHVSCAQAAGVMMQPDDWPFVVFITCFRHKIPNLERAKGALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELPKRVKSRLSVASDMRFNEIFTEKEVKQEKKRQRVINSRYREDYIEPALYRAIME 4A811BEECFEDC6B3 jmjd2a-h3_peptide 2 3 unspecified role unspecified role neutral component neutral component lys 4 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation certain certain sequence position certain certain certain sequence position certain lys 4 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain lys 4 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain ala1 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain arg2 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain thr3 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain gln5 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role neutral component neutral component tudor domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain trp 967 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr973 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain phe932 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr942 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp945 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asn940 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain gln937 sufficient to bind sufficient binding region sufficient to bind x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain ecobb Escherichia coli (strain B / BL21) 16 8 18 9 10 19 20 11 12 21 13 22 17 7 direct interaction direct interaction 2C, table S1 crystal structure of the double tudor domain of JMJD2A both in the presence and absence of a trimethylated H3-K4 peptide (H3K4Me3). 2.1A working 22.4, free 27.0 jmjd2a-h3_peptide-1 1 4 unspecified role unspecified role neutral component neutral component O75164:p.Trp967His mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain W H Wed May 02 19:41:35 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'trp967his' Tue Jun 30 19:43:04 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Trp967His' O75164:p.Tyr973Ala mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain Y A Wed May 02 19:38:28 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'tyr973ala' Tue Jun 30 17:51:38 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Tyr973Ala' O75164:p.Asp945Arg mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain D R Wed May 02 17:53:28 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'asp945arg' Tue Jun 30 19:42:00 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Asp945Arg' tudor domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 3 unspecified role unspecified role neutral component neutral component lys 4 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation certain certain sequence position certain certain certain sequence position certain arg2ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain R A region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 3A, 3B Changing Tyr973 to an alanine (Y973A) or Trp967 to a histidine (W967H) abolishes the binding of H3K4Me3, whereas the wild-type double tudor domain binds the peptide with an apparent equilibrium dissociation constant (Kd) of 10.4 �M. The binding constants were determined using surface plasmon resonance (SPR) (Fig. 3, A and B).