Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria

2025-04-02 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2020-03-22 2020-04-08 2020-05-13 2025-04-02 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM103310 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM111980 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM132120 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R21 AI119672 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM116799 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM103310 United States Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria Tan YZ Zhang L Glycosyltransferase, lipomannan, lipoarabinomannan, arabinofuranose, membrane protein, nanodisc, single-particle cryo-electron microscopy, acyl carrier protein Tan YZ Zhang L Rodrigues J Zheng RB Giacometti SI Rosario AL Kloss B Dandey VP Wei H Brunton R Raczkowski AM Athayde D Catalao MJ Pimentel M Clarke OB Lowary TL Archer M Niederweis M Potter CS Carragher B Mancia F Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol.Cell US 78 683 2020 32386575 doi:10.1016/j.molcel.2020.04.014 1097-2765 2168 MOCEFL 6w98 FULLOVERLAP Wild-type Mycobacterial Arabinofuranosyltransferase AftD Complexed with Acyl Carrier Protein Wild-type Mycobacterial Arabinofuranosyltransferase AftD Complexed with Acyl Carrier Protein 0 1 2 0.050 F5/8 type C domain-containing protein 1 1 Mycobacteroides abscessus subsp. abscessus Acyl carrier protein 1 2 Escherichia coli (strain K12) F5/8 type C domain-containing protein Mycobacteroides abscessus subsp. abscessus 0.14958428099999999 1 Escherichia coli LEVO SYVMTYRLDSSALSRRWLAVAAAVSLLLTFSQSPGQISPDTKLDLAINPLRFAARALNLWSSDLPFGQAQNQAYGYLFPH GAFFSLGHLLGVPAWVTQRLWWALLIVAGFWGLIRVAEALGIGTRGSRIIAAVAFALSPRVLTTLGAISSETLPMMLAPW VLLPLILTFQGRMSPRRAAALSAVAVALMGAVNAVATALACGVAVIWWLAHRPNRTWWRFTAWWIPCLALASTWWIVALL IFGKISPKFLDFIESSGVTTQWTSLTEVLRGTDSWTPFVAPTATAGSSLVTQSAMVIATTMLAAAGMAGLAMRGMPARGR LVAVLLIGLVLLTAGYTGALGSPIAQQIQFFLDDGGTPLRNVHKLEPLIRLPLILGLAHALSRIPLPASVPVRQWLSALA RPERNRAVAFAIVLLVALAASTSLAWTGRLVPRGGFDAIPGYWNDTAHWLADHDTGGRALVVPGAPFAIQTWGLTRDEPL QALGQTPWGVRDSIPLTPPETIRAIDSVQQLFAAGRPSDGLADTLREQGISYLVVRNDLDPDTSRSARPILVHHTIEGSP GLTKVAQFGDPVGAGAVEGFVADSDLRPQYPAVEIYAVGANDHDGEPYFTDIDTMPRVAGGPEALLRLNERRRQLNEPPL GPSLLATDAAQAGLRPGPAVVTDTPLARETDYGRVDDHSSAIRAPGDKRRTFNRVPDYPATGVPLVNGSWTGGTITASSS ASDSTALPNVAPGTSTAAAIDRDNATSWVSSSLEAALGQWIRIDLDRPITNAILTVTPSATALGAQVRRLEVETDNGTTS VRFDEPGQPLNIALRPGETTWVKVTATGTDDGTSGVQFGVTELSLTQYDAAGFAHTVDLRHSATVPPPPAGDNPLGWDLG SPLQGRSGCAPSPQRLRCAATLSLAPEEPGTFIRTLTVPQPVSLTPRLWVRARPGPQLRDLIQQPGTTVATGDSDVIDPQ GSSYAATDGDPGTVWTAPQDSVQRLHLPSLVIKLPKPTAIGAIRLRPSRTEVPAHPKQVAINLGDGPQLRSIDPKADVTE LALHPSITDTITVTVTDWTDIIDRTALGFDQLKPPGIAEVIALDADHRPIAPADNAANSKRKITIGCNRGPILALAGRFV PMSITATVRELLDGTVIQATPCDTSPIATGAGIQDVTVNPSQQFIVDGVQLTAAATEPASATMTVAPKGAWGPDRREVTA EPSAHERVLAVPESINPGWAARDAQGHLLTPVRVNGWQQGWVLPAGDGGKITLTFGLNTWYRAGLFGGLALLPILACLAL LPARGRTTLPPVAPWCAGPAAGVAVLAALTAISGISGMAVGLAALAFKVWTRWPLRAVTAAGVYLAGGSLLLAGAALSRH PWRSVGGYTGHSWWIQLLALISVASVALAAVRLPSRRCWKRRSASREGDSTSA A0A1N1NKH9 Acyl carrier protein Escherichia coli (strain K12) K12 0.008645459999999999 1 LEVO MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA P0A6A8 CALCIUM ION 4.0078e-05 2 CA [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate 0.0007179959999999999 1 6OU 4'-PHOSPHOPANTETHEINE 0.000358348 1 PNS water 1.8015e-05 1 HOH singleParticle particle 1 7.5 20.0 C8H18N2O4S HEPES 200.0 NaCl Sodium Chloride

Solution was filtered and degassed.

Homemade COPPER CARBON HOLEY PLASMA CLEANING 15 OTHER ETHANE 298 SPOTITON

The Spotiton V1.0 robot was operating at room temperature and moderate humidity..

Protein was incorporated into lipid nanodiscs.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 15 GATAN K2 QUANTUM (4k x 4k) COUNTING 3838 3710 1-90 4 7274 13.05 95.72 1

Energy filter slit width of 15 eV was used during the collection and was aligned automatically every hour using Leginon.

2800102 Ab initio model

Ab initio model was generated in CryoSPARC

C1 2.9 FSC 0.143 CUT-OFF RELION 2.1 490616 MAXIMUM LIKELIHOOD cryoSPARC 2

Non-uniform refinement in CryoSPARC was used.

MAXIMUM LIKELIHOOD cryoSPARC 2

Non-uniform refinement in CryoSPARC was used.

7 400015.0 RELION 2.1

RELION 3D Classification was used to separate out junk

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