Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn

2025-05-14 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-04-26 2025-05-14 2025-05-14 2025-05-14 Not funded Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1 Orlova EV Isupov MN Baseplate cup, baseplate wedge, fibers, VIRUS Orlova EV Isupov MN Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1 To Be Published 0353 9f4a FULLOVERLAP vB_Kpn_Lilla1 vB_Kpn_Lilla1 0 3 4 5 6 7 8 9 10 12 2 1 vB_Kpn_Lilla1 Klebsiella VIRION OTHER false false Long tail fiber proximal subunit Klebsiella phage KP1 0.138688438 18 LEVO MSDLLKQHFRATNGLDAGGNKVINVALADRNVKTDGVSVEYVIQENTIQKYDPTRGYLTDFAVTYGRRIWIANKDIPKPA GDFNQANWTSLRVDPNWIYTVRKGEFEIQSGQFINVDSNAAGNATLLLPLAPDEGDTIVVRDIGGRPGYNGILIKAQDTG ASIVFGESRLREVRLTRPYSQIMLTFSNGAWRASLTDFGDTAKMVVPNGIVPTQVQSGDNVVRRYTSNSEIFITLPLFAN SNDIINFTDLDGTSPINHMTVRTFDPTISIGTPGQTEIQVRTSGNGFLVYDSIDKIWRIFENDLRTRVRIITSDVTLMPN EHISVFGTDNNTVKTINVTLPTDVAVGDTVTIAMNYMRKGQTVVIKASGGDTIASNLNLLQFPKRSEYPPDAAWVQSSSI TFNGTTSYVPVLELAYIEEKATGKSYWIITESDPTVERVDAKDNTTRARLGVIALATQAQANAESNAEKELAITPETLNG RRSTETQTGIARIATSSEVNQSTTASYLDNVIVTPKKLNERAATETRRGLAEIASNAKMDAGTDDFTIVTPKKLLYRTTS DSRLGVVQLVKTGGAPNTTNDRSSAGTGIFDHSDYKNAVTPKTLREYKATVNQSGIVWLATDSEVRNGTPASSNIPTVVT PEALHKKVATDGAIGLIQIATQTEVNAGGVTNKAVTPKTLNDRTATNDRTGIARFATPGAQGEFEAGTSSTVMVNPKLLF DKFANTGRIQVNTSSGLTITGNLWDHYTINIQEASTSQRGTTTLATAAEVRTGTDAKKIVTAATLHAKTATEGAIGLAQY ATQAQVDAGTLSDRIVPPAYLKQTIQVTESWQATDSVRGTVRLSTGDGTWKGNDTNGSTLPDNGYASKGVAVSPYELNLT LKHYLPRLGKAYDTGMLGGQTPDKYARRDIAQTISGAWSFSQDTSFSNNISVQNIIYANGGEVKISPTADTGNVHVRFQN RDGSERGIIYAEPQTASAGTLKIRVKNGTGTTAASQTYTFGGNGTLEVPNEVSTKTLRSSGNAIVGGTVMVKDVQMLAVE GLNSIFGAQSQSAFIRSRDADTQIFAQDSTGSYPILTTKNYARLADGRYVKKAGDTMTGNLNINSSAIVITGSESWYVPT NETVIRQGSWTAEIKDATKLKGLRGYMVPIRTPIDPANPSTLVVTGYEEKTAAGGVLTQIGVTTNNTYQLWTPYPPTTET ADKRFAHTVWMRIYNPNLNKFDDWMRVFTSATPPTAADIGAPSSVSTQVKTLEVLEWIKLGPVKIWPDRPNQTLKFEWVG D A0A5B9NKG2 Baseplate tail tube cap Klebsiella phage KP1 0.038263663999999996 6 LEVO MIFEELADGLENIKKSGTRISQGKSKLTNAPTTKVAQFPAERSAGNDSAQDMRVHDLYRNGLLFTAYDFKGRTTPDLRSF RRDVMLSSVFDSPMSALANSSSSTTSTAPVANILLPRSKSDVDSVSHKFNDVGDSLVTRGGGTATGVLSNVASTAVFGSI ESLTQGLMADNGEQIYNTARSMYAGPDNRTKVFTWDLTPRSADDLIQIIRIYEIFNYYSYGVTGNSSYAKEVKAAIDEWY KGTLKSAAPDGAKVENTVFEQITSFLSNVIVVSNPTIWTVRNFGYSTSMDGREDIFGPCQIQSIRFDKTPNGHFNGLAIA PNLPSTFTLEITMREILTLNRGNVYIGGIE A0A2K9V618 Baseplate subunit Klebsiella phage KP1 0.033716129 6 LEVO MFTLEEFKSQAADIDFQRTNMFSVVFATVPSSKTQALLNDFGGELYNNMGLDGNWLGLTPGEFNQGITTIVTQGTRQVVR KSGVNTFMIGAMTQRVVQSLLGEFTVGTYLLDFFNMAFPTAGLMVYSAKIPENRLSYEMDKFHNAPNIKITGRDMEPLVL SFRMDPEASNYRAMQDWVNAVEDPVTGLRGLPQDVECDIQVNLHARNGLPHTVCLFSGAMPVACGAPEFTYDGENTIAVF DVTFAYRSMQTGSVGKQAAMDWLEDKAIQKIETINPNQGLSASASRLSRLGGAGGGISNITTTTSRII A0A7I8V4E3 Baseplate wedge protein gp6 Klebsiella phage KP1 0.07368924199999999 12 LEVO MAIKEPLNYQLTRTANAIPDAFTGATFDEIKNQLINWLSGQKEFQDFDFAGSRLNVLLDLLAYNTLYIQQFGNTALYESF IGTANLRSSVVQAAQQNGYLPSSKSAATASIMLEVTHPNPEPAIKIPRGTKFLAYARDSSVDPYNFVVTENVIALRDTSA PEGVNRYLPIVNLAQGRIIRTQLSYDPKKPIVIRDQSIDRKQVKLWVDGAEWTNWTDRSMVHASSISTIYYMRETVDGNT EFFFGEGVAEASVAGGVLESNFIGGLKPTKGAQVVIEYIRTDGESANGATDFSYADTLQYIVVNKIIENWSDSPDYVGAD GGGEPEDIERIRELAQIKRESQMRCVSKTDYESFVSSRFGSIVQAVQCFTDQDKPGYAFIAIKPKSGLQLTAVQREDIQD YLRPFCLAPITPSVMSPDYLFIRHNIKASYALNKLQESEQWLQSKIIDSINRYYVDEVEMFNKNFSKSKLLTYIDDTDHS IIGSSVDIQMVREIVNYFTLPSAGIKYYNTITPRTLRSGDLVFTVTPTADSYPVNIVGTDPDKNGKGNMVIGPFKPGDIK ENTHIQPYTEDDFDRTTNGERTRWYKIGEVDYYGDNIYWSLGAIGADPLQFEDQSIELYSTPTQDIVFARDGTLIVFEND LRPQYTTIKLEPITQ A0A2K9V5R4 Baseplate wedge protein gp7 Klebsiella phage KP1 0.119645719 6 LEVO MTIAPFVTSLRIHKLSANQVNIRWDDVGANFYYFVELAETRNRAGEVIPADNLSWSSLGYTADNDWFEQNRIEPLTYYKM RVQTTSAGFEPSEWVETEEFQTFEENAYTFEHMQEFSLVKEFIKQKFSLNNMSYVNFNTSAMMASLMTESFQFSPEYSHL SAIENFVVGESGYHEIQGPIEAVCVDKNRTMLGEIDGILYLFERFQHMVKVSNDKGQNWQYVQLFNDRVGNPVSRVVIYQ SKTTSYVLGYDKIFYGRKSSDVRWSSNEVKFSDNEVTFAKLGDQLKLGFEVELFGTYASLPADVTKYAEAFTCNDDYLYV VAKDTVRKVKLKDAPIDTDPLSPTFGEKVFEKEVSHITGNPKSVCFKMDSVGGKIFALITGEVKTLGLDPTDPRNVVDSA TKGVYVYQEGTNTWKRVFGNTDEEKRRIEHLWTSMSTDGKEIFFSSANFKTTEYAQDIELETKYPELISTAVKNVNPIQY HSDKHYHMMSFRADEFSRWETFVPGPMRFYAEPWFVWMAREGNRCWISTADHAVVIYNDILYQKRVDAAAQGTTERILSE VWDKGDATFYCPPVSFNGFLQYASGIMFHEPDGKLIGYYAFDYRVRDQVTLNWKPTDVMFKAFLQNQTREEDWTPEHTPG LRDPDLRPYLTKMMPDSYLLQDSNFEHFCKYYLQFLSDGNGTHYNSLVNLVKNKYPREENAWEYLWSEVYKRNIYLSKDA RDAVVRFFEARKNDFYATKGIEDSYKFLFKLLYNEDVEIDIESKNTTEYDIIVESTNISDDLVGRTIYTASGRSNVTYIE REYRDGRLLWRITIHNLSGRFIEGQEIKSERTDFEGIIVQGVRGKDMLSNNIDYINRSRSYYVMKIKSQLPTSRFRDDVL RFVHPVGFGFIGITLLTMFINSGLNMKHVETIINKLKNYKWDAGLPSVYPDRVAIIASDDTIERDPITNEPRYSSRAQAG EPFPLPANYNQENNNSVIAGQNPGQRRKPLSPTFDQSAVTFANYRDLVNQRLKDDAGNPRDPENPTQVKIDE A0A2K9V5T9 Baseplate wedge subunit Klebsiella phage KP1 0.038704387 12 LEVO MSNSTRASSTRSTIYRAIITSKFRTEKMYTFYKSIGPGTDQNTLYVSFGKSTPWSDNESEPGFAPPYPADNEDGVVDIWT NMMGAVKIESSMLDCVVPRRDWGDTRYPNPRTFLIGDIVVANSAPYNRTDAGFGWMVYRCIDVPKNGMCSIGNLTSKEEC IKLGGKWTPSTISGSAPRGRGDANGTVDLGDGYLWEYLYEIPADVSINRCTNEYIVVPWPEEIEESPARWGFQNNLTWQQ NDFNLIYRMKCNTIRFKAYLDAVYFPEFSLPGNTGFRQLSIITNPLEVKPMPNSPNVKAEKGWYSASGLERQSGEMIYME NRQPIIRSMDQTEELNLIFEF A0A2Z4QAY9 Baseplate wedge tail fiber connector Klebsiella phage KP1 0.032380195 18 LEVO MYTDKGKKIIDVGEIGNASTGDILYDGGVKINDNFDAIYNAFADQRLFAAGGGALNQKIHATSYYQKIKFGDANSAGTVP MGSCIDADCSEGAVQIRLSKGKAGEAVFVVNSNGSASKARSIKITTNGEGVADAFKDGSRELIINTPRCRIELWCVEVKA NGAAVWDYSISSMFGSTYSPLEATYNLTSSPINIRLGYNDDYSTVKLLLSFSANPGGQTIKRQSSEVMLMIDPTITSSAP NGRVFDTEYAVLRSGESSENEKMYSISYSINAQKDLICTASTSYGNARLAVKVIATQTVGVSQ A0A2K9V5S1 Baseplate wedge protein gp10 Klebsiella phage KP1 0.06671207 18 LEVO MKQNLIVGQSVDDGSGDYLRKGGLKINNNFDDLYSELGDGSVPFAAGAWKTFKASPTGTTLNAKFGQAFAINTQAARVNV QLPKGTANDYNKVIKLRDVWSTWRLSPITVIPAQGDTLKGSASPKIFNTNFQDLELVYCAPGRWEYIENKTVDKLTNGNL STVAKKSIIATAGQTDFLNIFDGVEYNEDSLNVYRRGNILYYGETSVMDKANADYGSPGTVAGQLVELNGKDIRLKVPCV EGEVITFETFLDGIGVYRSSYNKLAIQIRDSAQTTSQTIPGSMIVDNLATLRRITLDDMGVLPGVGVNPNSLEISLNGKE LLEAGTAGLPLFYCEGAEGGYAEDCINNGGQWVNSNQDYRLEFDSTGTNVEAIIFGEAFEDKDLLTVRWFNNNIGTTMDI DDIMAETDQVYMNAEQLVTLKNRIEYTNYDEPNQKNMRPVADDIMIKVNNIAAFFDVIYPIGTIYENAHNHANPADYMGF GVWKLYSQGRVTAGWNNDSSDPYFSRNNNNLNENGQPSLTAGGTVGDLTFTLGKEHIPELMSRDKVLISDPEHGSVVIGG CQLDPDAQGPGYSKYREDTVAVNNGVVPNDITKIQPTITVYRWIRVG A0A2K9V5S8 Tail sheath protein Klebsiella phage KP1 0.071695094 42 LEVO MPLVSPGIELKETSVQSTVVLNATGRAAIVGKFQWGPAYQVTQITNEVELVDMFGGPNNQTADYFMSAMNFLQYGNDLRT VRVVNREAAKNASPLVDNIEWEITTAGSNYEVGDKITVKYADQVVDDTGSVTEVDSDGKIKSVFIPTSKIIAYAKSINQY PDLGSSWTTTITSQSSGVSAVITLGKIISDSTVLLTEPETAHEEMTKTEFQTALAKYKMPGIVAAYPGELGNQLEIEIVS KAAFDKGEQLTIYPAGGKRASTAKAVFGYGPQTDTQYAIIVRRDGAVVESAVLSTSRQDKDIYGNNIFMDDYFSKGSSRY IFATAQGWPEGFAGVIRLGGGVSANESVTAGDLIQGWDLFGDREALRVNLLIAGACAGETDEIASTVQKHVSSIADERQD CLALISPPRSTIVNIPLTRAVDNLIDWRQGEGSYDSANMNINTTYAAIDGNYKYQYDKYNDVNRWVPLAADIAGLCARTD DIAQPWMSPAGYRRGQILNCIKLAIEPRQAHRDRMYQAGINPVTGQGTGDGFILFGDKTATTVPTPFDRINVRRLFNMLK NNIGDSSKWQLFELNDNFTRSSFRMETSQYLAGIKALGGVYDFRVVCDTTNNTPAVIDRNEFVASFYIKPARSINYITLN FVATATGADFDELIGP A0A2K9V5S7 Tail tube protein Klebsiella phage KP1 0.018633738 36 LEVO MELTDITRAFESGDFARPNLFEVEIPYLGRNFSFKCKAAPMPAGIVEKVPVGYMNRKINVAGDRTYDDWTVTIYNDDKHE VRKAIIAWQAQAHAQGNDISGMTPADYKKVATVRQFSRDGKTITNEHTITGLWPTNVGEVQMDWDSNNEVETFETTFAID WWE A0A2K9V5T6 IraD/Gp25-like domain-containing protein Klebsiella phage KP1 0.01538236 6 LEVO MSNIDKLYSDLDPEMRLAWDTDVSKTVGARSVKNSLLGIITTRKGSRPFDPEFGCDITNELFENMTPLTGDTIKRNIVSA VRNYEPRINRLSVDVLPLYDDNAIIVTVQFSIVDDPDTLERIRIQMRSNANSSSRV A0A0K1Y5J2 Putative baseplate hub subunit Klebsiella phage KP1 0.043526016 3 LEVO MTTQRLGYPNISIKLYSGYDAWLANRFVELAATFITLTMRDSLRGTNEGLLQFYDSKNMHTRMNGDELVQISVANSNTSR TQTRIYGIKHFTVGVDDKGDSIITLQLGTLHDIMNLKFSRAFFSSAYETIKEMIGAMYVDQPLIAPPINGINAYVPRVPW TSTLKDYLRYVRNVGISTDNDQFIFAWEDITGINMMDYESMISQDPNVFMFGAPQTIGQFAAGLKYPLAWDFEWLVKSNR YNRNPMKNATFYAHSFVDKDVTRIINGEGQNSVFINRSGGYSDMIFRNGYEEALRISTMAQYDGYAQTKCYGNFELTPGM KINFVDLKDQFRTDFYIDEVIHEISNNTSITNLYMFTNGSALEPVDLIKVKNELKRDSSY A0A7T3TJP2 Baseplate wedge subunit Klebsiella phage KP1 0.024693419999999997 6 LEVO MLFSFFSPIDYSAKTVKGAKAKAIPTADIFRNYRKYFDTVAENYLLQTYYISGAPRPEELAYILYGNSQLYWILLMCNNV YDPFRDWIKTQDACYQFAQQKYADVGGDQILYHVDANGNRYYNLEQYPENSGIWYDKGDFNHQYPQYTGALAGVDIYEDS IIENEKLRQINIINPSDIEAFLSDIIREMEKAPDSEYESGRYKSQTTIGEVL A0A2K9V5R5 Baseplate central spike protein Klebsiella phage KP1 0.063317457 3 LEVO MIEMNDSLKWFTGVVEDRQDPLKQGRVRVRVYGLHPFEKVQGAITGLPTEDLPWMSVIQPTNSAGISGVGSSITGMVEGT SVFGLWLDEFKTAGLVIGTYSAHRKTKPNYTEGFSDPTGQYPRQVGSDTNPLVQGDETGYSAIPNIIQDRNLDIGINPDD ADLSDIPEDPNPAITITDMLNRDEGLRLKVYWDTEGYPTVGIGHLIMAQKVRDMSVINKTLSNQVGRTVTGNPGIITMDE AVALFKQDRDKMLSDIKTNSRVGPVYAKVNKSRQMALENMSFQMGVGGLAKFGKMLDAMLIGDWKTAYTEARNSVWFNQT KGRASRVSMIILTGNMESYGVPAPKPEGKNLSAAYVEPKSGGNPEDPWTPEDSRILFKEPESSYNGQYPYVHTMETESGH IQEFDDTPGYERYRIVHPTGSYEEVAPDGRRTRKTVADLYDMTQGDGNILISGDKKVNVGGNETYYNMYNRRQQIDGDNT LYVRGNETKTIEGDGTIFVKGNIKIVVEGNADIQVNGDATTKVDGNHDVTVGGNLTWQVAGTVNWNVGGAWTETMASMSS IAQGQYTVDGSRIDVG A0A976LXP5 3.2.1.17 CHLORIDE ION 3.5453e-05 1 CL singleParticle particle 7.5

100mM NaCl, 8mM MgSO4, 50mM Tris-HCl

EMS Lacey Carbon COPPER 400 CARBON LACEY 300.0 ETHANE 92.0 281 FEI VITROBOT MARK IV

Klebsiella phage KP1 variant vB_Kpn_Lilla1

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.5 2.5 81000.0 83505.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 78.7 93.6

Alignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron detector model*: post GIF K3

GATAN K3 (6k x 4k) COUNTING 4092 5760 4 2.0 40.0 1 34529 PHASE FLIPPING AND AMPLITUDE CORRECTION C6 FOURIER SPACE 3.95 FSC 0.143 CUT-OFF 2415 OTHER MAXIMUM LIKELIHOOD 200 60.0 emd_50186.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -0.29478946 0.5440083 0.004389434 0.03993818 1.067 1.067 1.067 0.16 AUTHOR ::::EMDATABANK.org::::EMD-50186:::: FLEXIBLE FIT REAL emd_50186_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -0.20186959 0.4123014 0.0042892625 0.035573952 1.067 1.067 1.067 AUTHOR ::::EMDATABANK.org::::EMD-50186:::: C3 map to 4.33 A resolution used to rebuild monomers with C3 symmetry, particularly gp199. emd_50186_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -2.9412868 2.7837214 0.0016364073 0.2742179 1.067 1.067 1.067 AUTHOR ::::EMDATABANK.org::::EMD-50186:::: emd_50186_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -2.594944 2.2363303 0.0015330028 0.26977837 1.067 1.067 1.067 AUTHOR ::::EMDATABANK.org::::EMD-50186::::