Cryo-EM density map corresponding to BcsRQAB subcomplex

2021-02-24 REL PDBe PDBe PDBe 2020-10-13 2021-02-24 2021-02-24 2021-02-24 ATIP-Avenir 2016 France European Research Council (ERC) Biomatrix 757507 France Centre National de la Recherche Scientifique (CNRS) France European Institute of Chemistry and Biology (IECB) France Cryo-EM density map corresponding to BcsRQAB subcomplex Zouhir S Abidi W Zouhir S Caleechurn M Roche S Krasteva PV Architecture and regulation of an enterobacterial cellulose secretion system. Sci Adv US 7 2021 33563593 doi:10.1126/sciadv.abd8049 2375-2548 EMD-10799 other EM volume EMD-11356 other EM volume EMD-11836 associated EM volume Cryo-EM density map corresponding to BcsR2Q2AB subcomplex obtained after local refinement within the assembled Bcs macrocomplex(BcsRQABEF-BcsMacrocomplex.mrc). Cryo-EM density map corresponding to BcsR2Q2AB subcomplex obtained after local refinement within the assembled Bcs macrocomplex(BcsRQABEF-BcsMacrocomplex.mrc). 0 1 2 3 4

Bcs macrocomplex was purified using recombinant co-expression of constructs pRSFDuet1-Bcs(Strep)E-F-G and pCDFDuet1-Bcs(His)R-Q-A(HA-FLAG)-B and affinity pull-down using an anti-FLAG M2 resin (Sigma). The proposed stoichiometry for the resultant assembly is BcsR2-Q2-E2-F2-A-B(5-6). Densities corresponding to a BcsR2Q2AB subcomplex were improved after particle subtraction and local refinement in cryoSPARC V2. BcsE and BcsF partake in the assembled Bcs macrocomplex, BcsG does not co-purify stably with the macrocomplex.

Escherichia coli 1094 Inner membrane Escherichia coli BL21(DE3) pRSFDuet1-Bcs(Strep)EFG and pCDFDuet1-Bcs(His)RQA(HA-FLAG)B 0.257 Bacterial cellulose synthase regulator protein BcsB Escherichia coli 1094

Genome-encoded BcsB harbors a signal sequence to be addressed to the periplam where according to the ServerP4.1 server prediction would result in a mature form starting with the residue #26 TPATQ BcsB sequence was cloned in a pCDFDuet1 vector along Bcs(His)R, BcsQ and BcsA(HA-FLAG). 1 copy in locally refined BcsR2Q2AB map, up to 6 copies in the assembled Bcs macrocomplex.

Escherichia coli BL21(DE3) LEVO TPATQPLINAEPAVAAQTEQNPQVGQVMPGVQGAD APVVAQNGPSRDVKLTFAQIAPPPGSMVLRGINPNGSIEFGMRSDEVVTKAMLNLEYTPS PSLLPVQSQLKVYLNDELMGVLPVTKEQLGKKTLAQMPINPLFITDFNRVRLEFVGHYQD VCENPASTTLWLDVGRSSGLDLTYQTLNVKNDLSHFPVPFFDPRDNRTNTLPMVFAGAPD VGLQQASAIVASWFGSRSGWRGQNFPVLYNQLPDRNAIVFATNDKRPDFLRDHPAVKAPV IEMINHPQNPYVKLLVVFGRDDKDLLQAAKGIAQGNILFRGESVVVNEVKPLLPRKPYDA PNWVRTDRPVTFGELKTYEEQLQSSGLEPAAINVSLNLPPDLYLMRSTGIDMDINYRYTM PPVKDSSRMDISLNNQFLQSFNLSSKQEANRLLLRIPVLQGLLDGKTDVSIPALKLGATN QLRFDFEYMNPMPGGSVDNCITFQPVQNHVVIGDDSTIDFSKYYHFIPMPDLRAFANAGF PFSRMADLSQTITVMPKAPNEAQMETLLNTVGFIGAQTGFPAINLTVTDDGSTIQGKDAD IMIIGGIPDKLKDDKQIDLLVQATESWVKTPMRQTPFPGIVPDESDRAAETRSTLTSSGA MAAVIGFQSPYNDQRSVIALLADSPRGYEMLNDAVNDSGKRATMFGSVAVIRESGINSLR VGDVYYVGHLPWFERLWYALANHPILLAVLAAISVILLAWVLWRLLRIISRRRLNPDNE Bacterial cellulose synthase protein BcsA Escherichia coli 1094

BcsA sequence was cloned in pCDFDuet1 vector along with Bcs(His)R, BcsQ and BcsB. BcsA harbours a C-terminus HA-Flag Tag. 1 copy in both the locally refined BcsR2Q2AB complex and the assembled Bcs macrocomplex.

Escherichia coli BL21(DE3) LEVO MSILTRWLLIPPVNARLIGRYRDYRRHGASAFSATLGCFWMILAWIFIPLEHPRWQRIRAEHKNLYPHINASRPRPLDPVRYLIQTCWLLIGASRKETPKPRRRAFSGLQNIRGRYHQWMNELPERVSHKTQHLDEKKELGHLSAGARRLILGIIVTFSLILALICVTQPFNPLAQFIFLMLLWGVALIVRRMPGRFSALMLIVLSLTVSCRYIWWRYTSTLNWDDPVSLVCGLILLFAETYAWIVLVLGYFQVVWPLNRQPVPLPKDMSLWPSVDIFVPTYNEDLNVVKNTIYASLGIDWPKDKLNIWILDDGGREEFRQFAQNVGVKYIARTTHEHAKAGNINNALKYAKGEFVSIFDCDHVPTRSFLQMTMGWFLKEKQLAMMQTPHHFFSPDPFERNLGRFRKTPNEGTLFYGLVQDGNDMWDATFFCGSCAVIRRKPLDEIGGIAVETVTEDAHTSLRLHRRGYTSAYMRIPQAAGLATESLSAHIGQRIRWARGMVQIFRLDNPLTGKGLKFAQRLCYVNAMFHFLSGIPRLIFLTAPLAFLLLHAYIIYAPALMIALFVLPHMIHASLTNSKIQGKYRHSFWSEIYETVLAWYIAPPTLVALINPHKGKFNVTAKGGLVEEEYVDWVISRPYIFLVLLNLVGVAVGIWRYFYGPPTEMLTVVVSMVWVFYNLIVLGGAVAVSVESKQVRRSHRVEMTMPAAIAREDGHLFSCTVQDFSDGGLGIKINGQAQILEGQKVNLLLKRGQQEYVFPTQVARVMGNEVGLKLMPLTTQQHIDFVQCTFARADTWALWQDSYPEDKPLESLLDILKLGFRGYRHLAEFAPSSVKGIFRVLTSLVSWVVSFIPRRPERSETAQPSDQALAQQGSARSSGRTGLEFEEFYPYDVPDYAADYKDDDDKRS Bacterial cellulose synthase regulator protein BcsR Escherichia coli 1094

BcsR sequence was cloned in pCDFDuet1 vector along with BcsQ, BcsA(HA-FLAG) and BcsB. BcsR harbours a N-terminal octahistidine tag (N-His8). Likely two copies in the assembled secretion complexes, however the local resolution does not allow backbone tracing. High-resolution structures solved by X-ray crystallography.

Escherichia coli BL21(DE3) LEVO MGSSHHHHHHHHAAGSMNNNEPDTLPDPAIGYIFQNDIVALKQAFSLPDIDYADISQREQLAAALKRWPLLAEFAQQK Bacterial cellulose synthase regulator protein BcsQ Escherichia coli 1094

BcsQ sequence was cloned in pCDFDuet1 vector along with Bcs(His)R, BcsA(HA-FLAG) and BcsB

Escherichia coli BL21(DE3) LEVO MAVLGLQGVRGGVGTTTITAALAWSLQMLGENVLVVDACPDNLLRLSFNVDFTHRQGWARAMLDGQDWRDAGLRYTSQLDLLPFGQLSIEEQENPQHWQTRLSDICSGLQQLKASGRYQWILIDLPRDASQITHQLLSLCDHSLAIVNVDANCHIRLHQQALPDGAHILINNFRIGSQVQDDIYQLWLQSQRRLLPMLIHRDEAMAECLAAKQPVGEYRSDALAAEEILTLANWCLLNYSGLKTPVGSKS singleParticle particle 0.8 8.0 0.2 HEPES 0.12 NaCl 0.005 MgCl2 2e-06 AppCp 2e-06 c-di-GMP 0.008 LM.NPG Quantifoil R1.2/1.3 GOLD GLOW DISCHARGE

Elmo Glow Discharge system

ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.75 2.75 130000.0 GIF Quantum LS GATAN K2 SUMMIT (4k x 4k) COUNTING 1.2 1

Data collection at the CM01 line in ESRF Grenoble (Titan Krion, GATAN K2 Summit DED and Quantum LS Imaging filter).

Particle picking using cryoSPARC's template picker and 2D classes generated from an initial dataset collected on the Elsa the Talos Arctica at the IECB Bordeaux.

Gctf

Gctf through the cryoSPARC v2 interface

Ab initio model generation in cryosparc V2 C1 4.5 FSC 0.143 CUT-OFF cryoSPARC 2

Two rounds of local refinement of the BcsR2Q2AB assembly were performed using different fulcrum placements. The resulting maps gave FSC values of ~3.9 and 4.1A, respectively, as determined by cryoSPARC using the 0.143 cut-off. The unsharpened maps were combined and conservatively sharpened to 4.5 A resolution. The sharpened map was used for building the C-terminal tail-anchor of BcsB and flexible fitting of a Robetta-derived homology model of BcsA. A BcsR2Q2 dimer solved by X-ray crystallography was rigid-body fitted in the apical density.

173294 MAXIMUM LIKELIHOOD cryoSPARC v2

All 2D classification, particle curation, ab initio model generation, particle subtraction and local refinement were performed in cryosparc v2

MAXIMUM LIKELIHOOD cryoSPARC v2 cryoSPARC v2

3D variability analysis

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