2024-05-29 REL RCSB RCSB RCSB 2020-09-16 2021-07-28 2021-07-28 2024-05-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM100888 United States Structure of T7 DNA ejectosome periplasmic tunnel Swanson N Cingolani G T7, ejectosome, ejection protein, genome-delivery, podoviridae, VIRAL PROTEIN Swanson NA Lokareddy RK Li F Hou CD Leptihn S Pavlenok M Niederweis M Pumroy RA Moiseenkova-Bell VY Cingolani G Cryo-EM structure of the periplasmic tunnel of T7 DNA-ejectosome at 2.7 angstrom resolution. Mol.Cell US 81 3145 2021 34214465 doi:10.1016/j.molcel.2021.06.001 1097-2765 2168 MOCEFL 7k5c FULLOVERLAP Multisubunit T7 DNA ejectosome periplasmic tunnel with 6x copies of Gp15 and 6x copies of Gp16 Multisubunit T7 DNA ejectosome periplasmic tunnel with 6x copies of Gp15 and 6x copies of Gp16 0 1 2 Escherichia phage T7 0.59 Internal virion protein gp15 Escherichia phage T7 0.084454008 6 Escherichia coli LEVO MSKIESALQAAQPGLSRLRGGAGGMGYRAATTQAEQPRSSLLDTIGRFAKAGADMYTAKEQRARDLADERSNEIIRKLTP EQRREALNNGTLLYQDDPYAMEALRVKTGRNAAYLVDDDVMQKIKEGVFRTREEMEEYRHSRLQEGAKVYAEQFGIDPED VDYQRGFNGDITERNISLYGAHDNFLSQQAQKGAIMNSRVELNGVLQDPDMLRRPDSADFFEKYIDNGLVTGAIPSDAQA TQLISQAFSDASSRAGGADFLMRVGDKKVTLNGATTTYRELIGEEQWNALMVTAQRSQFETDAKLNEQYRLKINSALNQE DPRTAWEMLQGIKAELDKVQPDEQMTPQREWLISAQEQVQNQMNAWTKAQAKALDDSMKSMNKLDVIDKQFQKRINGEWV STDFKDMPVNENTGEFKHSDMVNYANKKLAEIDSMDIPDGAKDAMKLKYLQADSKDGAFRTAIGTMVTDAGQEWSAAVIN GKLPERTPAMDALRRIRNADPQLIAALYPDQAELFLTMDMMDKQGIDPQVILDADRLTVKRSKEQRFEDDKAFESALNAS KAPEIARMPASLRESARKIYDSVKYRSGNESMAMEQMTKFLKESTYTFTGDDVDGDTVGVIPKNMMQVNSDPKSWEQGRD ILEEARKGIIASNPWITNKQLTMYSQGDSIYLMDTTGQVRVRYDKELLSKVWSENQKKLEEKAREKALADVNKRAPIVAA TKAREAAAKRVREKRKQTPKFIYGRKE P03725 Peptidoglycan transglycosylase gp16 Escherichia phage T7 0.144028219 6 Escherichia coli LEVO MDKYDKNVPSDYDGLFQKAADANGVSYDLLRKVAWTESRFVPTAKSKTGPLGMMQFTKATAKALGLRVTDGPDDDRLNPE LAINAAAKQLAGLVGKFDGDELKAALAYNQGEGRLGNPQLEAYSKGDFASISEEGRNYMRNLLDVAKSPMAGQLETFGGI TPKGKGIPAEVGLAGIGHKQKVTQELPESTSFDVKGIEQEATAKPFAKDFWETHGETLDEYNSRSTFFGFKNAAEAELSN SVAGMAFRAGRLDNGFDVFKDTITPTRWNSHIWTPEELEKIRTEVKNPAYINVVTGGSPENLDDLIKLANENFENDSRAA EAGLGAKLSAGIIGAGVDPLSYVPMVGVTGKGFKLINKALVVGAESAALNVASEGLRTSVAGGDADYAGAALGGFVFGAG MSAISDAVAAGLKRSKPEAEFDNEFIGPMMRLEARETARNANSADLSRMNTENMKFEGEHNGVPYEDLPTERGAVVLHDG SVLSASNPINPKTLKEFSEVDPEKAARGIKLAGFTEIGLKTLGSDDADIRRVAIDLVRSPTGMQSGASGKFGATASDIHE RLHGTDQRTYNDLYKAMSDAMKDPEFSTGGAKMSREETRYTIYRRAALAIERPELQKALTPSERIVMDIIKRHFDTKREL MENPAIFGNTKAVSIFPESRHKGTYVPHVYDRHAKALMIQRYGAEGLQEGIARSWMNSYVSRPEVKARVDEMLKELHGVK EVTPEMVEKYAMDKAYGISHSDQFTNSSIIEENIEGLVGIENNSFLEARNLFDSDLSITMPDGQQFSVNDLRDFDMFRIM PAYDRRVNGDIAIMGSTGKTTKELKDEILALKAKAEGDGKKTGEVHALMDTVKILTGRARRNQDTVWETSLRAINDLGFF AKNAYMGAQNITEIAGMIVTGNVRALGHGIPILRDTLYKSKPVSAKELKELHASLFGKEVDQLIRPKRADIVQRLREATD TGPAVANIVGTLKYSTQELAARSPWTKLLNGTTNYLLDAARQGMLGDVISATLTGKTTRWEKEGFLRGASVTPEQMAGIK SLIKEHMVRGEDGKFTVKDKQAFSMDPRAMDLWRLADKVADEAMLRPHKVSLQDSHAFGALGKMVMQFKSFTIKSLNSKF LRTFYDGYKNNRAIDAALSIITSMGLAGGFYAMAAHVKAYALPKEKRKEYLERALDPTMIAHAALSRSSQLGAPLAMVDL VGGVLGFESSKMARSTILPKDTVKERDPNKPYTSREVMGAMGSNLLEQMPSAGFVANVGATLMNAAGVVNSPNKATEQDF MTGLMNSTKELVPNDPLTQQLVLKIYEANGVNLRERRK P03726 4.2.2.- water 1.8015e-05 219 HOH singleParticle particle 2.2 8.5 100.0 Tris/HCl Tris buffer 10.0 MgCl2 magnesium chloride 100.0 Na3C6H5O7 sodium citrate
Solutions were made fresh and filtered.
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 120.0 GLOW DISCHARGE AIR 0.03 ETHANE 95 278 FEI VITROBOT MARK IV
blot for 6 seconds before plunging.
This sample was monodisperse, but high concentration. Some preferred orientation.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 1.0 2.5 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 8601 3.4 50.0 1 4700000
Manually picked 2000 particles using Relion GUI, followed by 2D-Classification to select templates, then Relion auto-picking was used.
Generated ab initio with Relion-3.0-b from this dataset
 2 C1 2.7 FSC 0.143 CUT-OFF RELION 3.0-b 208024 MAXIMUM LIKELIHOOD RELION 3.0-b
RELION
 MAXIMUM LIKELIHOOD RELION 3.0-b
RELION
 6 75000.0 RELION 3.0-b emd_22680.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 380.16 380.16 380.16 90.0 90.0 90.0 X Y Z -0.17808002 0.2799669 -0.0000007178213 0.0076619512 1.08 1.08 1.08 0.0267 EMDB Post-process map from Relion-3.0 AB INITIO MODEL 0.92 REAL 45.100000000000001