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/ http://www.ebi.ac.uk/ liu-2006-2 Structure of the human Papillomavirus E7 oncoprotein and its mechanism for inactivation of the retinoblastoma tumor suppressor. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Liu X., Clements A., Zhao K., Marmorstein R. Apoptosis - Interactions involving proteins with a function related to apoptosis It was not possible to identify the E7 protein from the HPV geneotype 16 used in this study and therefore data relating to this protein was not entered. marmor@wistar.upenn.edu J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation BioCreative - Critical Assessment of Information Extraction systems in Biology liu-2006-1 Structure of the human Papillomavirus E7 oncoprotein and its mechanism for inactivation of the retinoblastoma tumor suppressor. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Liu X., Clements A., Zhao K., Marmorstein R. Apoptosis - Interactions involving proteins with a function related to apoptosis marmor@wistar.upenn.edu J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation BioCreative - Critical Assessment of Information Extraction systems in Biology rb_human Retinoblastoma-associated protein pRb pp110 p105-Rb RB1 p110-RB1 protein protein human Homo sapiens Human MPPKTPRKTAATAAAAAAEPPAPPPPPPPEEDPEQDSGPEDLPLVRLEFEETEEPDFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQKKKELWGICIFIAAVDLDEMSFTFTELQKNIEISVHKFFNLLKEIDTSTKVDNAMSRLLKKYDVLFALFSKLERTCELIYLTQPSSSISTEINSALVLKVSWITFLLAKGEVLQMEDDLVISFQLMLCVLDYFIKLSPPMLLKEPYKTAVIPINGSPRTPRRGQNRSARIAKQLENDTRIIEVLCKEHECNIDEVKNVYFKNFIPFMNSLGLVTSNGLPEVENLSKRYEEIYLKNKDLDARLFLDHDKTLQTDSIDSFETQRTPRKSNLDEEVNVIPPHTPVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSKDREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPKKKGSTTRVNSTANAETQATSAFQTQKPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRLKTNILQYASTRPPTLSPIPHIPRSPYKFPSSPLRIPGGNIYISPLKSPYKISEGLPTPTKMTPRSRILVSIGESFGTSEKFQKINQMVCNSDRVLKRSAEGSNPPKPLKKLRFDIEGSDEADGSKHLPGESKFQQKLAEMTSTRTRMQKQKMNDSMDTSNKEEK ve7_hpv1 Protein E7 E7 protein protein hpv1a Human papillomavirus type 1a Human papillomavirus type 1a MVGEMPALKDLVLQLEPSVLDLDLYCYEEVPPDDIEEELVSPQQPYAVVASCAYCEKLVRLTVLADHSAIRQLEELLLRSLNIVCPLCTLQRQ e2f1_human Transcription factor E2F1 Retinoblastoma-associated protein 1 Retinoblastoma-binding protein 3 PBR3 E2F1 RBBP3 pRB-binding protein E2F-1 protein protein human Homo sapiens Human MALAGAPAGGPCAPALEALLGAGALRLLDSSQIVIISAAQDASAPPAPTGPAAPAAGPCDPDLLLFATPQAPRPTPSAPRPALGRPPVKRRLDLETDHQYLAESSGPARGRGRHPGKGVKSPGEKSRYETSLNLTTKRFLELLSHSADGVVDLNWAAEVLKVQKRRIYDITNVLEGIQLIAKKSKNHIQWLGSHTTVGVGGRLEGLTQDLRQLQESEQQLDHLMNICTTQLRLLSEDTDSQRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAVDSSENFQISLKSKQGPIDVFLCPEETVGGISPGKTPSQEVTSEEENRATDSATIVSPPPSSPPSSLTTDPSQSLLSLEQEPLLSRMGSLRAPVDEDRLSPLVAADSLLEHVREDFSGLLPEEFISLSPPHEALDYHFGLEEGEGIRDLFDCDFGDLTPLDF e2f3_human Transcription factor E2F3 E2F3 KIAA0075 protein protein human Homo sapiens Human MRKGIQPALEQYLVTAGGGEGAAVVAAAAAASMDKRALLASPGFAAAAAAAAAPGAYIQILTTNTSTTSCSSSLQSGAVAAGPLLPSAPGAEQTAGSLLYTTPHGPSSRAGLLQQPPALGRGGSGGGGGPPAKRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQLLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLKDQTVIVVKAPPETRLEVPDSIESLQIHLASTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPASKDLASTNSGHSDCSVSMGNLSPLASPANLLQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEEEGISDLFDAYDLEKLPLVEDFMCS q6h1d8_9aden Early E1A protein E1A protein protein human adenovirus e Human adenovirus E MRHLRDLPDEEIIIASGSEILELVVNAMMGDDHPEPPTPFETPSLHDLYDLEVDVPEDDPNEKAVNDLFSDAALLAAEEASSPSSDSDSSLHTPRHDRGEKEIPGLKWEKMDLRCYEECLPPSDDEDEQAIQNAASHGVQAVSESFALDCPPLPGHGCKSCEFHRINTGDKAVLCALCYMRAYNHCVYSPVSDADDETPTTESTLSPPEIGTSPSDNIVRPVPVRATGRRAAVECLDDLLQGGDEPLDLCTRKRPRH e7-rb Pulldown analysis reveals interaction between E7 protein and retinoblastoma tumour-suppressor protein 493713 N/A 493715 unspecified role unspecified role prey prey undefined mutation lys810glu lys814glu lys824glu mutation disrupting mutation disrupting interaction mutation disrupting 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 undefined mutation lys814glu lys824glu lys828glu lys830glu mutation disrupting mutation disrupting interaction mutation disrupting 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 certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 493716 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P06465:p.Glu74_Glu75delinsArgArg mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 4 The authors demonstrate that muation lys810glu within the Rb protein C terminus restored binding of the E7 mutant (glu74arg glu75arg). The autors state that the E7 (amino acid residues 44-93) and Rb protein (amino acid residues 803-841) failed to show interaction but do not provide the data for this assertion. e2f3-rb Pulldown analysis reveals interaction between E2F3 protein and retinoblastoma-associated protein 493713 N/A 493717 unspecified role unspecified role prey prey c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 1.0 N/A 493715 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 physical association physical association false false false Figure 5 e7-e2f3 Pulldown analysis reveals interaction between the E7 protein and E2F3 protein 493713 N/A 493718 unspecified role unspecified role prey prey c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 493716 unspecified role unspecified role bait bait n terminal gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P06465:p.Arg60Glu mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false P06465:p.Leu61Glu mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 6 e2f3-rb-1 Pulldown analysis reveals interaction between E2F3 protein and retinoblastoma-associated protein 493713 N/A 493717 unspecified role unspecified role prey prey c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 493719 inhibitor inhibitor ancillary ancillary region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 493715 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) association association false false false Figure 5 Adenovirus E1A-CR1CR2CR3 (amino acid residues 1 to 189) (accession number Q6H1D8) was shown to disrupt the interaction of E2F3 protein and Rb protein e2f3-rb-2 Pulldown analysis reveals interaction between E2F3 protein and retinoblastoma-associated protein 493713 N/A 493717 unspecified role unspecified role prey prey c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 493716 inhibitor inhibitor ancillary ancillary region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 493715 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) association association false false false Figure 5 The E7 protein (amino acid residues 44 to 93) (accession number P06465) was shown to disrupt E2f3 interaction with the Rb protein. Although the E7 protein (amino acid residues 16 to 93)was shown to be more potent in disrupting the interaction. e7-e7 Structural determination of E7 homodimer 493714 N/A 493716 unspecified role unspecified role neutral component neutral component asn62 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val84 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false ser80 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false asn82 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false asn82 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu81 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false met76 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val59 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false ile83 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val48 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu73 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val63 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu61 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 493716 unspecified role unspecified role neutral component neutral component leu64 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false thr62 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false asp66 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu64 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false gln72 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val48 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val59 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false val63 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu77 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu73 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu61 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false leu81 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false ile83 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false met76 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 493777 493763 493778 493766 493779 493765 493780 493764 493781 493768 covalent binding covalent binding false false false Figure1. Table 1. 1.6 R working = 20.8% R free = 25.2% Residues that contribute to this dimer-induced core include dyad-related interactions from Val-48 from beta-1, Val-59, Leu-61, and Val-63 from beta-2, Leu-73, Met-76, and Leu-77 from beta-1, and Leu-81 and Ile-83 from beta-3. The carbonyl oxygens of Thr-62 and Leu-64 from one protomer make main chain hydrogen bonds to the amide groups of Asn-82 and Val-84 from the other protomer, and the amide groups of Leu-64 and Asp-66 from one protomer make hydrogen bonds to the carbonyl oxygens of Ser-80 and Asn-82 from the other protomer. An additional hydrogen bond is formed between the side chain of Gln-72 and the side chain of Met-76 from the other protomer. Finally, beta-3 from one protomer makes anti-parallel beta-strand interactions with the end of beta-2 of the other subunit.