Tail tip of siphophage T5 : full structure

2024-10-16 REL PDBe PDBe PDBe 2022-04-29 2023-02-08 2023-02-08 2024-10-16 Agence Nationale de la Recherche (ANR) ANR-16-CE11-0027 France Agence Nationale de la Recherche (ANR) ANR-21-CE11-0023 France Tail tip of siphophage T5 : full structure Linares R Arnaud CA Effantin G Darnault C Epalle N Boeri Erba E Schoehn G Breyton C Bacteriophage, Siphophage, T5, baseplate, VIRAL PROTEIN Linares R Arnaud CA Effantin G Darnault C Epalle NH Boeri Erba E Schoehn G Breyton C Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation. Sci Adv US 9 eade9674 eade9674 2023 36961893 doi:10.1126/sciadv.ade9674 2375-2548 7zqb FULLOVERLAP Escherichia virus T5 Escherichia virus T5 0 1 2 3 4 5 6 7

Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d

Escherichia virus T5 Escherichia coli F VIRUS-LIKE PARTICLE STRAIN false false Probable central straight fiber Escherichia phage T5 0.07485170299999999 3 LEVO MISNNAPAKMVLNSVLTGYTLAYIQHSIYSDYDVIGRSFWLKEGSNVTRRDFTGIDTFSVTINNLKPTTTYEVQGAFYDS IIDSELLNAQIGINLSDKQTFKMKSAPRITGARCESEPVDVGVGAPIVYIDTTGEADYCTIELKDNSNANNPWVKYYVGA LMPTIMFGGVPIGSYKVRISGQISLPDGVTIDSSGYYEYPNVFEVRYNFVPPAAPINIVFKAARIADGKERYDLRVQWDW NRGAGANVREFVLSYIDSAEFVRTGWTKAQKINVGAAQSATIISFPWKVEHKFKVSSIAWGPDAQDVTDSAVQTFILNES TPLDNSFVNETGIEVNYAYIKGKIKDGSTWKQTFLIDAATGAINIGLLDAEGKAPISFDPVKKIVNVDGSVITKTINAAN FVMTNLTGQDNPAIYTQGKTWGDTKSGIWMGMDNVTAKPKLDIGNATQYIRYDGNILRISSEVVIGTPNGDIDIQTGIQG KQTVFIYIIGTSLPAKPTSPAYPPSGWSKTPPNRTSNTQNIYCSTGTLDPVTNQLVSGTSWSDVVQWSGTEGVDGRPGAT GQRGPGMYSLAIANLTAWNDSQANSFFTSNFGSGPVKYDVLTEYKSGAPGTAFTRQWNGSAWTSPAMVLHGDMIVNGTVT ASKIVANNAFLSQIGVNIIYDRAAALSSNPEGSYKMKIDLQNGYIHIR Q6QGF0 L-shaped tail fiber protein p132 Escherichia phage T5 0.015079863999999998 12 LEVO MSTENRVIDLVVDENVPYGLLMQFMDVDDSVYPSTSKPVDLTDFSLRGSIKSSLEDGAETVASFTTAIVDAAQGVASISL PVSAVTTIASKASKERDRYNPRQRLAGYYDVIITRTAVGSAASSFRIMEGKVYISDGVTQ Q7Y5D9 Minor tail protein Escherichia phage T5 0.034367605 3 LEVO MFYSLMRESKIVIEYDGRGYHFDALSNYDASTSFQEFKTLRRTIHNRTNYADSIINAQDPSSISLAINFSTTLIESNFFD WMGFTREGNSLFLPRNTPNIEPIMFNMYIINHNNSCIYFENCYVSTVDFSLDKSIPILNVGIESGKFSEVSTFRDGYTIT QGEVLPYSAPAVYTNSSPLPALISASMSFQQQCSWREDRNIFDINKIYTNKRAYVNEMNASATLAFYYVKRLVGDKFLNL DPETRTPLIIKNKYVSITFPLARISKRLNFSDLYQVEYDVIPTADSDPVEINFFGERK Q6QGE3 Distal tail protein Escherichia phage T5 0.022798640999999998 6 LEVO MRLPDPYTNPEYPGLGFESVNLVDNDPMIRDELPNGKVKEVKISAQYWGINISYPELFPDEYAFLDSRLLEYKRTGDYLD VLLPQYEAFRVRGDTKSVTIPAGQKGSQIILNTNGTLTGQPKAGDLFKLSTHPKVYKITNFSSSGNVWNISLYPDLFITT TGSEKPVFNGILFRTKLMNGDSFGSTLNNNGTYSGISLSLRESL Q6QGE8 Tail tube protein Escherichia phage T5 0.050459214999999995 6 LEVO MSLQLLRNTRIFVSTVKTGHNKTNTQEILVQDDISWGQDSNSTDITVNEAGPRPTRGSKRFNDSLNAAEWSFSTYILPYK DKNTSKQIVPDYMLWHALSSGRAINLEGTTGAHNNATNFMVNFKDNSYHELAMLHIYILTDKTWSYIDSCQINQAEVNVD IEDIGRVTWSGNGNQLIPLDEQPFDPDQIGIDDETYMTIQGSYIKNKLTILKIKDMDTNKSYDIPITGGTFTINNNITYL TPNVMSRVTIPIGSFTGAFELTGSLTAYLNDKSLGSMELYKDLIKTLKVVNRFEIALVLGGEYDDERPAAILVAKQAHVN IPTIETDDVLGTSVEFKAIPSDLDAGDEGYLGFSSKYTRTTINNLIVNGDGATDAVTAITVKSAGNVTTLNRSATLQMSV EVTPSSARNKEVTWAITAGDAATINATGLLRADASKTGAVTVEATAKDGSGVKGTKVITVTAGG Q6QGE2 Pore-forming tail tip protein pb2 Escherichia phage T5 0.13162954699999999 3 LEVO MTDKLIRELLIDVKQKGATRTAKSIENVSDALENAAAASELTNEQLGKMPRTLYSIERAADRAAKSLTKMQASRGMAGIT KSIDGIGDKLDYLAIQLIEVTDKLEIGFDGVSRSVKAMGNDVAAATEKVQDRLYDTNRALGGTSKGFNDTAGAAGRASRA LGNTSGSARGATRDFAAMAKIGGRLPIMYAALASNVFVLQTAFESLKVGDQLNRLEQFGTIVGTMTGTPVQTLALSLQNA TNGAISFEEAMRQASSASAYGFDSEQLEQFGLVARRAAAVLGVDMTDALNRVIKGVSKQEIELLDELGVTIRLNDAYENY VKQLNATSTGIKYTVDSLTTYQKQQAYANEVIAESTRRFGYLDDALKATSWEQFAANANSALRSLQQSAATYLNPVMDTL NTFLYQTKSSQMRVSAMARSASAKTTPAENVTALIENAVGAREDLDTYLKESEERVKKAQELKQQLDDLKAKQAATAPIA NALTAGGIGGDESNKLVVQLTNELARQNKEIEERTKTEKVLRQAVQDTGEALLRNGKLAEQLGAKMKYADTAVPGDKGVF EVDPNNLKAVSEIQKNFDFLKKSSSDTANNIRMAASSITNAKKASSDLNSVVKAVEDTSKVTGQSADTLVKNLNLGFSSL DQMKAAQKGLSEYVTAMDKSEQNALEVAKRKDEVYNQTKDKAKAEAAAREVLLRQQQEQLTAAKALLAINPNDPEALKQV AKIETEILNTKAQGFENAKKTKDYTDKILGVDREIALLNDRTMTSTQYRLAQLRLELQLEQEKTELYSKQADGQAKVEQS RRAQAQISREIWEAEKQGTASHVSALMDALEVSQTQRNVTGQSQILTERLSILQQQLELSKGNTEEELKYRNEIYKTSAA LEQLKKQRESQMQQQVGSSVGATYTSTTGLIGEDKDFADMQNRMASYDQAISKLSELNSEATAVAQSMGNLTNAMIQFSQ GSLDTTSMIASGMQTVASMIQYSTSQQVSAIDQAIAAEQKRDGKSEASKAKLKKLEAEKLKIQQDAAKKQIIIQTAVAVM QAATAVPYPFSIPLMVAAGLAGALALAQASSASGMSSIADSGADTTQYLTLGERQKNVDVSMQASSGELSYLRGDKGIGN ANSFVPRAEGGMMYPGVSYQMGEHGTEVVTPMVPMKATPNDQLSDGSKTTSGRPIILNISTMDAASFRDFASNNSTAFRD AVELALNENGTTLKSLGNS Q7Y5E2 Probable baseplate hub protein Escherichia phage T5 0.107279766 3 LEVO MKKILDSAKNYLNTHDKLKTACLIALELPSSSGSAATYIYLTDYFRDVTYNGILYRSGKVKSISSHKQNRQLSIGSLSFT ITGTAEDEVLKLVQNGVSFLDRGITIHQAIINEEGNILPVDPDTDGPLLFFRGRITGGGIKDNVNTSGIGTSVITWNCSN QFYDFDRVNGRYTDDASHRGLEVVNGTLQPSNGAKRPEYQEDYGFFHSNKSTTILAKYQVKEERYKLQSKKKLFGLSRSY SLKKYYETVTKEVDLDFNLAAKFIPVVYGVQKIPGIPIFADTELNNPNIVYVVYAFAEGEIDGFLDFYIGDSPMICFDET DSDTRTCFGRKKIVGDTMHRLAAGTSTSQPSVHGQEYKYNDGNGDIRIWTFHGKPDQTAAQVLVDIAKKKGFYLQNQNGN GPEYWDSRYKLLDTAYAIVRFTINENRTEIPEISAEVQGKKVKVYNSDGTIKADKTSLNGIWQLMDYLTSDRYGADITLD QFPLQKVISEAKILDIIDESYQTSWQPYWRYVGWNDPLSENRQIVQLNTILDTSESVFKNVQGILESFGGAINNLSGEYR ITVEKYSTNPLRINFLDTYGDLDLSDTTGRNKFNSVQASLVDPALSWKTNSITFYNSKFKEQDKGLDKKLQLSFANITNY YTARSYADRELKKSRYSRTLSFSVPYKFIGIEPNDPIAFTYERYGWKDKFFLVDEVENTRDGKINLVLQEYGEDVFINSE QVDNSGNDIPDISNNVLPPRDFKYTPTPGGVVGAIGKNGELSWLPSLTNNVVYYSIAHSGHVNPYIVQQLENNPNERMIQ EIIGEPAGLAIFELRAVDINGRRSSPVTLSVDLNSAKNLSVVSNFRVVNTASGDVTEFVGPDVKLAWDKIPEEEIIPEIY YTLEIYDSQDRMLRSVRIEDVYTYDYLLTYNKADFALLNSGALGINRKLRFRIRAEGENGEQSVGWATI Q6QGE9 singleParticle particle 8.0 10.0 C4H11NO3 Tris 100.0 NaCl sodium chloride 1.0 MgCl2 magnesium chloride 1.0 CaCl2 calcium chloride Quantifoil R2/1 COPPER/RHODIUM 300 CARBON HOLEY ARRAY GLOW DISCHARGE 30

Intensity 25 mA

ETHANE 100 293.15 FEI VITROBOT MARK IV

3 uL of T5 tails sample (with or without FhuA-ND) were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0).

Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 3.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 40.0 1

low-resolution reconstruction from a previous data collection

C3 BACK PROJECTION 3.88 FSC 0.143 CUT-OFF RELION 3.0/3.1 9290 MAXIMUM LIKELIHOOD RELION 3.0/3.1 MAXIMUM LIKELIHOOD RELION 3.0/3.1 emd_14869.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 621.45996 621.45996 621.45996 90.0 90.0 90.0 X Y Z -0.04883774 0.11512272 0.00017022267 0.0024591512 1.351 1.351 1.351 0.028 AUTHOR ::::EMDATABANK.org::::EMD-14869:::: BACKBONE TRACE

Atomic protein models were built into the different cryo-EM maps using the Coot software by tracing the protein sequence into the densities and were then iteratively refined alternating Coot manual refinement and PHENIX real space refine tool until convergence. p140, p132, BHPpb3 and TMPpb2 C-ter models were built ab initio. For TTPpb6 and DTPpb9 models, already existing X-ray models (PDB codes 5NGJ / 4JMQ) were used as a starting point and were refined into the EM maps. Molprobity was used for model quality assessment.

REAL 40.0 emd_14869_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 621.45996 621.45996 621.45996 90.0 90.0 90.0 X Y Z -0.028484317 0.073736556 0.000038651895 0.002509438 1.351 1.351 1.351 AUTHOR ::::EMDATABANK.org::::EMD-14869:::: unsharpened map emd_14869_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 621.45996 621.45996 621.45996 90.0 90.0 90.0 X Y Z -0.047582228 0.09172043 0.00003759531 0.004381773 1.351 1.351 1.351 AUTHOR ::::EMDATABANK.org::::EMD-14869:::: emd_14869_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 621.45996 621.45996 621.45996 90.0 90.0 90.0 X Y Z -0.039505094 0.08981931 0.000047156347 0.0042558783 1.351 1.351 1.351 AUTHOR ::::EMDATABANK.org::::EMD-14869::::