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/ Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J. Biol. Chem. (0021-9258) 1995 imex curation Naktinis V., Onrust R., Fang L., O'Donnell M. odonnel@rockefeller.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Naktinis V., Onrust R., Fang L., O'Donnell M. Participant Detection method for dpo3b (DnaN) = scintillation counting odonnel@rockefeller.edu Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 1995 Only protein-protein interactions imex curation Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J. Biol. Chem. (0021-9258) 1995 imex curation Naktinis V., Onrust R., Fang L., O'Donnell M. odonnel@rockefeller.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Naktinis V., Onrust R., Fang L., O'Donnell M. odonnel@rockefeller.edu Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 1995 Only protein-protein interactions imex curation Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J. Biol. Chem. (0021-9258) 1995 imex curation Naktinis V., Onrust R., Fang L., O'Donnell M. odonnel@rockefeller.edu 18-Dec-2012: Contacted by IntAct-Help. 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 Naktinis V., Onrust R., Fang L., O'Donnell M. odonnel@rockefeller.edu Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 1995 Only protein-protein interactions imex curation dpo3b_ecoli Beta sliding clamp dnaN Beta-clamp processivity factor DNA polymerase III beta sliding clamp subunit JW3678 b3701 protein protein ecoli Escherichia coli (strain K12) MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL DIP protein P0A988 original sequence version: 48 This sequence has been withdrawn from Uniprot. 7A45646F61255B5A hola_ecoli DNA polymerase III subunit delta b0640 holA JW0635 protein protein ecoli Escherichia coli (strain K12) MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG 87239A678FE16BE2 87239A678FE16BE2 holc_ecoli DNA polymerase III subunit chi holC b4259 JW4216 protein protein ecoli Escherichia coli (strain K12) MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 7FEFFC359B28AA88 7FEFFC359B28AA88 dpo3x_ecoli DNA polymerase III subunit tau dnaX dnaZ dnaZX b0470 JW0459 DNA polymerase III subunit gamma protein protein ecoli Escherichia coli (strain K12) MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQAPTVPLPETTSQVLAARQQLQRVQGATKAKKSEPAAATRARPVNNAALERLASVTDRVQARPVPSALEKAPAKKEAYRWKATTPVMQQKEVVATPKALKKALEHEKTPELAAKLAAEAIERDPWAAQVSQLSLPKLVEQVALNAWKEESDNAVCLHLRSSQRHLNNRGAQQKLAEALSMLKGSTVELTIVEDDNPAVRTPLEWRQAIYEEKLAQARESIIADNNIQTLRRFFDAELDEESIRPI DIP protein P06710 original sequence version: 106 DIP protein P06710 original sequence version: null D2028BD99E375150 holb_ecoli DNA polymerase III subunit delta' holB b1099 JW1085 protein protein ecoli Escherichia coli (strain K12) MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL DIP protein P28631 original sequence version: 95 DIP protein P28631 original sequence version: null DC9DAA644AD8A096 hold_ecoli DNA polymerase III subunit psi holD b4372 JW4334 protein protein ecoli Escherichia coli (strain K12) MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND DIP protein P28632 original sequence version: 88 DIP protein P28632 original sequence version: null 5B7356201E7E27FE clamp-loading complex - hexamer 2 6 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Fig.s 1a, 5e S/U beta is sliding clamp, S/Us gamma, delta, delta', chi & psi make up clamp loader - all part of DNA Polymerase III complex clamp-loading complex - tetramer 2 7 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Fig. 1b clamp-loading complex - trimer 2 7 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Fig. 1c dnan-hola 2 4 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Fig. 2c, 5a, 5b this interaction is independent of ATP and MgCl2, ATP and MgCl2 are both needed for the full complex to form (see Fig. 5e+f) hola-dnan 3 5 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction Fig. 6a,b dnaN and dnaX (dpo3x) interact independently of the presence of ATP and MgCl2 when there rest of the gamma complex is missing (cf. Fig. 6c, d for binding to full gamma complex). In Fig.s 6c & d the rest of the gamma compound (dnaX, holB, holC and holD) were added after holA was immobilied and before dnaN was added. clamp-loading complex - hexamer 1 8 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component region 3h radiolabel 3h radiolabel 3H tritium H3 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association Fig.s 8a, 8e binding of DnaN, holC and holD to the rest of the gamma-complex requires ATP and MgCl2 in the buffer (cf. Fig. 5f, other panels of Fig. 8) S/U beta is sliding clamp, S/Us gamma, delta, delta', chi & psi make up clamp loader - all part of DNA Polymerase III complex