DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ richter-2016-1 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268825X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-2 ecolx Escherichia coli pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268823X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-3 human Homo sapiens Human anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268829X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-4 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268827X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-5 in vitro In vitro thermal shift thermal shift binding thermal shift predetermined predetermined participant predetermined Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268831X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-6 ecolx Escherichia coli pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268824X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-7 ecolx Escherichia coli pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268826X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-8 caeel Caenorhabditis elegans anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268830X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-9 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268828X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation richter-2016-10 ecolx Escherichia coli light scattering light scattering predetermined predetermined participant predetermined Richter H., Katic I., Gut H., Großhans H. DIP original experiment: DIP-268832X Nature structural & molecular biology 2016 IMEx Structural basis and function of XRN2 binding by XTB domains. Richter H., Katic I., Gut H., Großhans H. Only protein-protein interactions imex curation c2ail_human CDKN2AIP N-terminal-like protein CDKN2AIPNL CDKN2A-interacting protein N-terminal-like protein protein protein human Homo sapiens Human MVGGEAAAAVEELVSGVRQAADFAEQFRSYSESEKQWKARMEFILRHLPDYRDPPDGSGRLDQLLSLSMVWANHLFLGCSYNKDLLDKVMEMADGIEVEDLPQFTTRSELMKKHQS a0a0r4isj3_danre 5'-3' exoribonuclease xrn2 protein protein danre Danio rerio (Zebrafish) Brachydanio rerio Zebrafish MGVPAFFRWLSRKYPSIIVHCLEEKAKEYNGVKIPVDTSKPNPNEVEFDNLYLDMNGIIHPCTHPEDKPAPKNEDEMMVAIFEYIDRLFNIVRPRRVLYMAIDGVAPRAKMNQQRSRRFRASKEGVELAEEKQKMREEVIERGGYLPPEEIKERFDSNCITPGTEFMDNLAKCLRYYVADRLTNDPGWRNITVFLSDASVPGEGEHKIMDYIRRQRGQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIREEFKPNKPRPCALCSQMGHEIKDCQGLPREKQGEHDEFADTIPVSEQEFIFIRLAVLREYLERELTMASLPFPFSFERSVDDWVFMCFFVGNDFLPHLPSLEIREGAIDRLVGIYKDVVHKTGGYLTENGFVNLERVELIMQAVGVAEDNIFKKRKEDDESFKRRMKDKKKRMKAEQRPSFLPGGQFAPHALGGRDRPMAVQNARHAAFEMRMQGNQRNQDAAQSLRAMMRNGKGSAESSGSMDNRGVKRKADDSDSEPEPEDNVRLWEDGWKQRYYKTKFDVDATDDEFRKKVVQSYVEGLCWVLRYYYQGCASWKWYFPFHYAPFASDFKDIKGMFSDFEKGTKPFKPLEQLMGVFPAASGNFLPTTWRALMSDPESSIIDFYPDDFAIDLNGKKYAWQGVALLPFVDERRLRAALAEVYNDLTPEEVRRNSLGSDVMFVGRSHALCDFIQELYRAESHTATEIPAEFCHGIQGILNLDEDPILPDKLVESPIPVLRDISSNCAIGIKFKDPQYADGFVFKAVILPGAKIPNKVLKPGDWEQSNRGPWRPQLGFNPNRQQAHLDQSAFRKLNHHVGRSDGPGIYGSGPPSDAHRRGGAYSSAPPPTNYHQGNYRPPQRDHYSQSQSQYSRQPHMNTGSYPRFQQGSHGWDRAMQNQGSSYQQNQQRGRGDWRPQQNQQGFNSGRGYGLPPASRRYNWN q5xjm4_danre cdkn2aipnl zgc:101768 protein protein danre Danio rerio (Zebrafish) Brachydanio rerio Zebrafish MASMDVEEFIGQNRQLADRVEAFRGFSESDKHWKGRREFIFRNMADFPEPQVDHLLALSMVWQNHVFMGCRYSSELLQRVMEMAEGIEVEDAPVFKTRDEIIRQQKQR xrn2_human 5'-3' exoribonuclease 2 XRN2 DHM1-like protein protein protein human Homo sapiens Human MGVPAFFRWLSRKYPSIIVNCVEEKPKECNGVKIPVDASKPNPNDVEFDNLYLDMNGIIHPCTHPEDKPAPKNEDEMMVAIFEYIDRLFSIVRPRRLLYMAIDGVAPRAKMNQQRSRRFRASKEGMEAAVEKQRVREEILAKGGFLPPEEIKERFDSNCITPGTEFMDNLAKCLRYYIADRLNNDPGWKNLTVILSDASAPGEGEHKIMDYIRRQRAQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIREEFKPNKPKPCGLCNQFGHEVKDCEGLPREKKGKHDELADSLPCAEGEFIFLRLNVLREYLERELTMASLPFTFDVERSIDDWVFMCFFVGNDFLPHLPSLEIRENAIDRLVNIYKNVVHKTGGYLTESGYVNLQRVQMIMLAVGEVEDSIFKKRKDDEDSFRRRQKEKRKRMKRDQPAFTPSGILTPHALGSRNSPGSQVASNPRQAAYEMRMQNNSSPSISPNTSFTSDGSPSPLGGIKRKAEDSDSEPEPEDNVRLWEAGWKQRYYKNKFDVDAADEKFRRKVVQSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADMPSDFEKGTKPFKPLEQLMGVFPAASGNFLPPSWRKLMSDPDSSIIDFYPEDFAIDLNGKKYAWQGVALLPFVDERRLRAALEEVYPDLTPEETRRNSLGGDVLFVGKHHPLHDFILELYQTGSTEPVEVPPELCHGIQGKFSLDEEAILPDQIVCSPVPMLRDLTQNTVVSINFKDPQFAEDYIFKAVMLPGARKPAAVLKPSDWEKSSNGRQWKPQLGFNRDRRPVHLDQAAFRTLGHVMPRGSGTGIYSNAAPPPVTYQGNLYRPLLRGQAQIPKLMSNMRPQDSWRGPPPLFQQQRFDRGVGAEPLLPWNRMLQTQNAAFQPNQYQMLAGPGGYPPRRDDRGGRQGYPREGRKYPLPPPSGRYNWN xrn2_caeel 5'-3' exoribonuclease 2 homolog Y48B6A.3 xrn-2 protein protein caeel Caenorhabditis elegans MGVPAFFRWLTKKYPATVVNANEDRQRDQDGNRVPVDCTQPNPNFQEFDNLYLDMNGIIHPCTHPEDRPAPKNEDEMFALIFEYIDRIYSIVRPRRLLYMAIDGVAPRAKMNQQRSRRFRASKEMAEKEASIEEQRNRLMAEGIAVPPKKKEEAHFDSNCITPGTPFMARLADALRYYIHDRVTNDASWANIEIILSDANVPGEGEHKIMDYVRKQRGNPAHDPNTVHCLCGADADLIMLGIATHEANFNIIREEFVPNQPRACDLCGQYGHELKECRGAENETDLGDDYCKPEQREKNFIFLRIPVLREYLEKELSMPNLPFKFDVERALDDWVFLCFFVGNDFLPHLPSLEIREGAIDRLIKLYKEMVYQMKGYLTKDGIPELDRVEMIMKGLGRVEDEIFKRRQQDEERFQENQRNKKARMQMYGGGGRGGRGRGRGRGQQPAFVPTHGILAPMAAPMHHSGESTRQMASEARQTAMKFTNDANETAAANLKALLNVKGEESPADIASRKRKAEQPLIKPEEEEDEGPKDDIRLYESGWKDRYYRAKFDVGSDDIEFRHRVAWAYVEGLCWVLRYYYQGCASWDWYFPYHYAPFASDFETVGEFQPDFTRPTKPFNPLEQLMSVFPAASKQHLPVEWQKLMIQDDSPIIDLYPADFRIDLNGKKYAWQGVALLPFVDETRLLATLQSVYPTLTAEEKQRNTRGPNRIFIGRNHKSFEFFQQVAESKSDDLVPLDPTLLNGVSGKIAYDSTATAPGLPFVSPVNHDECQDLPTNCGICVLYEDPEYPQDYIFPALRLDGAKEPEKTLKPDDWNDRRDGRYQPQVGFNRNAPRGSLDQSGHRQVHHYVRGGGGGGGGYRGNSYDDRRGGGGGGGGYNDRQDFGRNYGGRDGGGPQRYHDQQQQRQGGYQGGGYGGGYGGGGGGGGGGGGGSYHQPYNQDQRRGGRGGGGGPPGYQRPPYRGGGGGGYHGNSSWR paxt1_caeel Partner of xrn-2 protein 1 paxt-1 R05D11.6 protein protein caeel Caenorhabditis elegans MGKLEDVEAEKKLWESDDAWELRKAFMLAHYDDYPKIQLQCLSQLFINVTLLGCEYSQTLMQKIRTMGAGIAANKDRTKTGSYVKASAAKKRQAVKTSDLEGASDESKKVKMEKSPSPVARESFDERLGKLKASLAMTPHHLTGEQMMKTATNSCLMKWHVNKINQKIEITIDRYVAFRHTFSQYCVDPRDCAINTLIESILSCDAAVHEESYEIRFDGVPVDECYAKSVTRRLAKIKSAVSNGAHTVKGLTTYLDAVNMSMIQNTQKLEGWSQQLDLVTADLLLSSRVLSSTECTKPAMATIANQMSEDVCQLILNDKINVINSMKSHSSLAFQ f1qzx8_danre cdkn2aip protein protein danre Danio rerio (Zebrafish) Brachydanio rerio Zebrafish MAARRGEDIVSEFLSQNPHLVSWVESLRGHCETNKQWYARREFVLRNMEAFPTIQPGSPSSSLDRLLSLSMVWANHVFLGCRYPQRVMDKINEMAEGITVIEAPERKTRDEIMGKLKRPAVSAADADYQGKKTKPNEPDDRAHSKCVVHPATSSHKCGPSPGAPAEHQPFFNRLYKAVAWKLVSAGGFGPNLEHFEILRSCVESCKASLTCVFVPLKDIPDLPAGRTQREGQVCELRCCTVYMGTGYGRDESAARAMASKEALKVFQGQKVTVKISRRRFRGRDVDDLVLLDEQSRSQAFPPALSCPFQEDE cdkn2aipnl-xrn2-1 3287947 N/A 3287957 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3287958 unspecified role unspecified role unspecified role unspecified role Region 1-803 Region 1-803 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false cdkn2aipnl-xrn2-2 3287948 N/A 3287958 unspecified role unspecified role prey prey Region 1-803 Region 1-803 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3287959 unspecified role unspecified role bait bait His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli physical association physical association false false false cdkn2aipnl-xrn2-3 3287949 N/A 3287960 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3287957 unspecified role unspecified role bait bait Q96HQ2:p.Tyr81Ala Y81A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false Flag-tag Flag-tag flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false HA-tag HA-tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Tag used for western blot detection. human Homo sapiens Human physical association physical association false false false paxt_1-xrn_2-1 3287950 N/A 3287961 unspecified role unspecified role unspecified role unspecified role Region 1-257/295-417/532-787 Region 1-257/295-417/532-787 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3287962 unspecified role unspecified role unspecified role unspecified role Region 1-75 Region 1-75 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false paxt_1-xrn_2-2 3287951 N/A 3287961 unspecified role unspecified role unspecified role unspecified role Region 1-257/295-417/532-787 Region 1-257/295-417/532-787 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3287962 unspecified role unspecified role unspecified role unspecified role Region 1-75 Region 1-75 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false cdkn2aip-xrn2-1 3287952 N/A 3287963 unspecified role unspecified role bait bait His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3287958 unspecified role unspecified role prey prey Region 1-803 Region 1-803 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli physical association physical association false false false paxt_1-xrn_2-3 3287953 N/A 3287961 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3287962 unspecified role unspecified role bait bait Q21738:p.Cys54Ala C54A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false Q21738:p.Tyr56Ala Y56A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli physical association physical association false false false cdkn2aipnl-xrn_2-1 3287954 N/A 3287961 unspecified role unspecified role prey prey caeel Caenorhabditis elegans N/A 3287957 unspecified role unspecified role bait bait Flag-tag Flag-tag flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false caeel Caenorhabditis elegans physical association physical association false false false paxt_1-xrn_2-4 3287955 N/A 3287961 unspecified role unspecified role unspecified role unspecified role Region 1-257/295-417/532-787 Region 1-257/295-417/532-787 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3287962 unspecified role unspecified role unspecified role unspecified role Region 1-75 Region 1-75 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false paxt_1-xrn_2-5 3287956 N/A 3287961 unspecified role unspecified role unspecified role unspecified role Region 1-257/295-417/532-787 Region 1-257/295-417/532-787 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3287962 unspecified role unspecified role unspecified role unspecified role Region 1-75 Region 1-75 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false