2024-11-13 REL PDBe PDBe PDBe 2022-07-12 2022-11-30 2022-11-30 2024-11-13 Wellcome Trust 202231/Z/16/Z United Kingdom Other private Vallee Scholarship Leverhulme Trust Philip Leverhulme Prize United Kingdom Structure of trimeric SlpA outer membrane protein von Kuegelgen A Bharat TAM SlpA protein, STRUCTURAL PROTEIN von Kugelgen A van Dorst S Alva V Bharat TAM A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. Proc.Natl.Acad.Sci.USA US 119 e2203156119 e2203156119 2022 35943982 doi:10.1073/pnas.2203156119 1091-6490 0040 PNASA6 8ae1 FULLOVERLAP Structure of trimeric SlpA protein Structure of trimeric SlpA protein 0 1
Structure of trimeric SlpA protein
Deinococcus radiodurans BAA-816 S-layer protein SlpA Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 0.12383536699999999 3 LEVO MKKSLIALTTALSFGLAAAQTAAPVSAPQVPALTDVPAGHWAKDAIDRLVSRGVILGYPDGTFRGTQNLTRYEAAIIIAR LLDQMRDGETPAGMTAEDMTALQNAIQELAADLAALGVRVSDLEANAVSKDDFARLEARIEEVAAAGGEQGATEALQGQI DDLTARVDEYDALRADVDDNASSIAALNDLTVLLNQDILDLQDRVSAVEAAQADFVQRSDFDALGGRVTTVETRVETVNN SLTGRIAALERNAFSVKPSLTIGYSVSRTSRNFDVDRLFPLNADGTVANNAFTSGGIDTDTGAQRRDFGDFGNASDPVVA GAAGLYGFADGVSYTVYFTDGSTATFDGLNPADYKVPTGKVIDTTKGRNGFGFNNLARYKEGSTDIGISLGFDTSGQFSQ VTSGTGGSLFSTAGRLQVNQIDLNFGLVTGLPSDAYVDTNGNGKKDDGEATGRGTYLGSGGTAAILRDPAGNVYRPVFFR FKNATTQFSVGNNPVIVTLGQQQKFYFSDYVFDNNYDGRGDGFTVTVDGSNVPVIGAWKPQIKGVYGSRSGLDGTAEAGY GVYYRGVRAQITPVGTLTAGIHYAQEGRDMFGAAQNTTSTPSDVTTYGADLHGKAFGVELHSEYATSRVRPNTANAAVQT SNAFYARVATRKDNLAFDLNTPAAKFGNDTFGVSLYDLNYRKIDAGYNNVAGISEYGYGSYSRTSAQNIAYNPDTGVTAP FANLDRQAYTDANNDGTSDRNADGTVVATNTKIGQMGFGVKAAANLGPVAIGGYYDTSTGANGDNANRMTEAGGSAKVAY SIFSLRGTYNTLDSNRPQIYRDAAGTQIIGDAKVRRYAVQADVTPGLGLFVGAYYRDVNVNGVRSTTDRGLLGRGYLASS FEPGVGNNAYRTGLRCADNNFGTGTRDIDGVGGVLNPAVNLDQSRTATCFTSYGVEAGHAGDNANALVKDLFFRVGYSRV YVPTTATATTGDFSGSVTYGDARYDRKVGVANVRLAGSFSTTNTQLDSRPAGTRGAVGLIVRTDPLENVPFRPQFNGQVG YYTADNRVAAGNYNANATKYGAGVVLNDFLLPQTKIGVRYDGYMAQNRQYTPFDGDGTQGYFSDANNNRRTNLNGVYVEG AYQDLIFSYGTYTLSQKDLNGVEYGSGINNGQPARGQTFKISYKVNF Q9RRB6 CALCIUM ION 4.0078e-05 18 CA singleParticle particle 4.45 7.5 20.0 C8H18N2O4S HEPES 150.0 NaCl Sodium chloride 0.02 C24H46O11 DDM
Buffer solutions were prepared fresh from sterile filtered concentrated stocksolutions. Solutions were filtered through a 0.22 um filter to avoid microbial contamination and degassed using a vacuum fold pump. The pH of the HEPES stock solution was adjusted with sodium hydroxide at 4 deg C.
 Quantifoil R2/2 COPPER/RHODIUM 200 CARBON HOLEY GLOW DISCHARGE AIR
20 seconds, 15 mA
 ETHANE 100 283.15 FEI VITROBOT MARK IV
Vitrobot options: Blot time 4.5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds.
Purified SlpA protein after size-exclusion chromatography
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 1.0 4.0 4.0 81000.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 GIF Bioquantum 20
EPU software with faster acquisition mode AFIS (Aberration Free Image Shift).
GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 2294 4.8 47.909 1
Movies were clustered into optics groups based on the XML meta-data of the data-collection software EPU (ThermoFisher) using a k-means algorithm implemented in EPU_group_AFIS (https://github.com/DustinMorado/EPU_group_AFIS). Imported movies were motion-corrected, dose weighted, and Fourier cropped (2x) with MotionCor2 (Zheng et al., 2017) implemented in RELION3.1 (Zivanov et al., 2018). Contrast transfer functions (CTFs) of the resulting motion-corrected micrographs were estimated using CTFFIND4 (Rohou and Grigorieff, 2015).
223878
Initially, micrographs were denoised using TOPAZ (73) using the UNET neural network and 2893 particles were manually picked. Particle coordinates were used to train TOPAZ picker (74) in 5 times downsampled micrographs with the neural network architecture ResNet8 and picked particles were extracted in 4 times downsampled 128 x 128 boxes and classified using reference-free 2D classification inside RELION3.1.
RELION de-novo
 1 C3 FOURIER SPACE 3.25 FSC 0.143 CUT-OFF RELION 3.1 122412 MAXIMUM LIKELIHOOD RELION 3.1
Angle assignment was performed within RELION3.1
 MAXIMUM LIKELIHOOD RELION 3.1
Angle assignment was performed within RELION3.1
 2 RELION 3.1
The reconstruction was further improved by Bayesian particle polishing, and a focused 3D-classification without refinement of the poses. The final output map was obtained from 122,412 particles, which was post-processed using a smooth mask focused on the trimeric OMBB including the first heptad of the coil coiled with a global resolution of 3.25 Angstrom according to the gold standard Fourier shell correlation criterion of 0.143.
 emd_15378.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 349.44 349.44 349.44 90.0 90.0 90.0 X Y Z -0.052389175 0.09440462 0.00001370914 0.0031721287 1.092 1.092 1.092 0.025 AUTHOR RELION PostProcessed map with B-factor sharpening AB INITIO MODEL Best Fit REAL 51.670000000000002 emd_15378_msk_1.map emd_15378_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 349.44 349.44 349.44 90.0 90.0 90.0 X Y Z -0.023005359 0.055638075 0.000013732971 0.002079392 1.092 1.092 1.092 AUTHOR Full map RELION without B-factor sharpening emd_15378_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 349.44 349.44 349.44 90.0 90.0 90.0 X Y Z -0.048077375 0.06291156 0.00001283038 0.0031346777 1.092 1.092 1.092 AUTHOR RELION Half map 1 emd_15378_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 349.44 349.44 349.44 90.0 90.0 90.0 X Y Z -0.036348876 0.06502154 0.000014561718 0.003124183 1.092 1.092 1.092 AUTHOR RELION Half map 1