2024-10-09 REL RCSB RCSB RCSB 2022-12-06 2023-02-22 2023-02-22 2024-10-09 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) PEW-00033055 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24GM129547 United States Chen J Bhabha G Ekiert DC Membrane protein complex, ABC transporter, Virulence factor, Lipid transport, MEMBRANE PROTEIN Chen J Fruhauf A Fan C Ponce J Ueberheide B Bhabha G Ekiert DC Nature UK 620 445 452 2023 37495693 doi:10.1038/s41586-023-06366-0 1476-4687 0006 NATUAS EMD-29023 other EM volume

Structure of Mce1-LucB complex from Mycobacterium smegmatis (Map1)

EMD-29025 other EM volume

Structure of Mce1 transporter from Mycobacterium smegmatis (Map0)

EMD-29238 other EM volume

Local refinement of MceG in Msmeg Mce1 transporter in the absence of LucB (Map2a)

EMD-29239 other EM volume

Local refinement of YrbE and MCE ring in Msmeg Mce1 transporter in the absence of LucB (Map2b)

EMD-29240 other EM volume

Local refinement of MCE ring and needle in Msmeg Mce1 transporter in the absence of LucB (Map2c)

EMD-29241 other EM volume

Local refinement of MCE needle and portal in Msmeg Mce1 transporter in the absence of LucB (Map2d)

EMD-29242 other EM volume

Raw, consensus refinement of Msmeg Mce1 transporter in the absence of LucB (Map2e)

8fee FULLOVERLAP Mce1 lipid transporter composed of Mce1 MCE proteins (Mce1ABCDEF) and an ABC transporter (YrbE1A-B, 2 copies of MceG) Mce1 lipid transporter composed of Mce1 MCE proteins (Mce1ABCDEF) and an ABC transporter (YrbE1A-B, 2 copies of MceG) 0 1 2 3 4 5 6 7 8 9

Complex was isolated directly from Mycobacterium smegmatis by pulling down MceG-GFP using GFP-affinity purification and size exclusion chromatography

Mycolicibacterium smegmatis MC2 155 Virulence factor Mce family protein Mycolicibacterium smegmatis MC2 155 0.043944491999999995 1 LEVO MTEPPAPTAPLNKPKTPPYKLAGLILGLVGVLVLALTWMQFRGQFEDKVQLTVLSGRAGLSMDPGSKVTFNGVPIGRLAS IDVVEVDDNPEARLTLDVDPKYLDLIPENANVELRATTVFGNKYISFLSPKNPSAERLSASTPIRAQGVTTEFNTLFETI TAISEQVDPIKLNETLTAAAQALDGLGDKFGRSIVDGNAILADVNPRMPQIRRDITGLANLGEVYADASPDLFDGLDNAV TTARTLNEQRGNLDQALVAAVGFGNTGGDIFERGGPYLVRGAQDLLPTSALLDEYSPALFCTIRNYHDAAPKLAGALGGN GYSLLTNSLVVGVGNPYVYPDNLPRVNAKGGPEGRPGCWQPITRDLWPFPYLVMDTGASIAPYNHFELGQPMFAEYVWGR QVGENTINP A0QNR2 Virulence factor Mce family protein Mycolicibacterium smegmatis MC2 155 0.037467737999999993 1 LEVO MSIKGTLFKLGIFSLVLLTFTALIFVVFGQIRFNRTTEYSAIFKNVSGLRDGQFVRAAGVEVGKVKSVDLINGGEQAEVK FTVERSLPLFQETTAAIRYQDLIGNRYLELKRGDSDQILPPGSTIPVERTEPALDLDALVGGFRPLFRSLEPEKVNTIAT SLITIFQGQGGTINDILDQTAQLTASLADRDQAIGEVIKNLNTVLDTTVRHQKQFDETLVNFETLITGLKNRADPIATSV ADISDAAGSLADLLSDNRPLLKDTIGYLDVIQAPLVEQKQEVSDILVQMPQALKIIGRAGGIYGDFFNFYACDLTLKLNG LQPGGPVRTVRITTQPSGRCTPK A0QNR3 MCE-family protein MCE1c Mycolicibacterium smegmatis MC2 155 0.054737805 1 LEVO MRTLQGSDRFRKGLMGVIVVALIIGVGSTLTSVPMLFAVPTYYGQFADTGGLNIGDKVRIAGMDVGNVKSMEIDGDKVVI GYTLGGRTIGTESRAAIRTDTILGRKNIEIEPRGSETLKPRGVLPVGQTSAPYQIYDAFLDVTRNAAGWDTQAVRQSLNV LSETVDQTSPHLSAALDGVARFSETIGKRDEDVKKLLASANKVATVLGDRSTQVNQLLVNAQTLLAAVNERGRSVSLLLE RVSSVSRQVEGFVDENPNLNHVLEQLRTVSDVLNERKQDLADILTVAGKFITSLAEALASGPYFKVMLVNLIPPTILQPF VDAAFKKRGIDPEEFWRNAGLPAFRFPDPNGERHENGAPPAAPTPLEGTPEHPGPAVPPGSPCSYTPPADGIPSPGNPLP CAHLSQGPYGPVPGGYPPPNVATSAPNPDGIAHSPGVPSAAIPGQMPPEQPGAPVEIAPGPPGARTVPVSPIPGAPDFTP GIAPPPPAITGPPPPPGPGPQLAPVGEAPLPGNPPFLPPGSQSR I7G2J2 Virulence factor mce family protein Mycolicibacterium smegmatis MC2 155 0.058054550999999996 1 LEVO MSTIFNIRNIQLPRLSRAAVIIGALVVAAALVAGYFGMNAYRKLTNTTVTAYFPEVLALYPGDKVLIMGVRVGSIDSIET AGDKMKVVFHFNNKYKVPENATASILNPSLVASRVIQLSPPYTGGPTLRDGAVLDVDRTQVPIEYDEVRNQVTRLLADLG PTPEQPKGPFGDIIESFADGFAGKGEQLNRTLRGLSDALTALNEGRGDFFAVVKSLALFVNALHRSDQQFVALNNDLAQF TNSFTNTDQELANALQDLNRVLKTTREFLDRNGGVLTHDIDNLEQVTTAILQPEPRDGLETGLHAYPNLAANVLNINSPN QGGIIGLPVLPGVTNFSNPLQFVCSSIQAGSRLGYQESAELCAQYLAPIMDAIKFNYLPFGMNLASTAMTLPKQIAYSEK RLQPPPGYKDTTVPGIWSRDTLFSHGNHEPGWIVAPGMQGVQVQPATANMLTPESLAELLGGPDIVPPPAPPAFGTTRGG NLPGPPNAFDENNPLPPPWYPQPGPPPAPAPGVIPGDPLSAVAPAAPAAPAAPAPAGPPLPAEAGAG A0QNR5 Virulence factor Mce family protein Mycolicibacterium smegmatis MC2 155 0.042566444999999994 1 LEVO MRLLKGFPKMRNWTRVGRRTAVLAAVALVLTSCGQWRGIANVPLPGGPGTESGSMTLYVQMPETLALNANSRVRVRDVFV GRVRKIELINWVPTLTVDVEPGIKLPKNTLAKIGQTSLLGSQHVELNPPEDPSSELLRDGDTIPLAQSSAYPTIERTLAG ISGILTGGGIPNIEVIQTEVFNILNGRADQIREFLNQLDTFTDELNQQREEITRAIDSTNRLLNIVSQRNDTLDRVLTEF PPLIQHFAETRDLFADAVTALGRLSAAADETLSGSNANLHTNLQNLQRPLKQLGRAAPYLVGALKLILTVPFNIDNIPKA IRGDYINVSLKLDLTLSSVDNAFLSGTGVSGMLRALEQAWGRDPATMIPDVRFTPNPHDAPGGPLVERGE A0QNR6 Mce-family protein mce1f Mycolicibacterium smegmatis MC2 155 0.054342898 1 LEVO MLLTRFIKMQLVIFLTLTLVALVVLALFYLRLPTWAGLGMYKLNADLPNSGGLYATANVTYRGTTIGKVTSVEPSESGAR VEMNIYDRYKIPADATANVHSVSAVGEQFIDLTSDSGGGAYFQPGDTITKATVPAEVGPALDAAEKGLAVLPKEKIGTLL DEAATAFGGLGPSLQRLVDSTQAIAGDFRANIDPVNDIIENSGPIIDSQVNSGDAIQRWAANLNTLAAQSAQNDEALRSG LQQAAPTADQLNAVFSDVRESLPQTLANLEIVIDMLKRYNKNVEQVLVALPQGAAVAQTGTIFAPEGLLHFGLGINAPPP CLTGFLPASQWRSPADTRTEPLPSGLYCKIPKDAPNAVRGARNYPCADVPGKRAATPRECRSDEPYQPLGTNPWYGDPDQ IRNCPAPGARCDQPVDPGRVIPAPSINNGLNPLPASQLPPPEVSSGPSSDPLTAPRGGTVTCSGQQPNPCIYTPAAGATA TYNPASGEVVGPGGVKYSVTNSNTPGDDGWKEMLAPAS A0QNR7 ABC transporter, ATP-binding protein,Green fluorescent protein chimera Mycolicibacterium smegmatis MC2 155 0.07162482

C-terminus of MceG is tagged (3C-eGFP-4xGly-Tev-Flag-His6)

2 LEVO MGVQIDVTGLSKSFGSSKIWEDVTMSIPAGEVSVLLGPSGTGKSVFLKSLIGLLRPERGSIVIDGTDILQCSAKELYEIR TLFGVLFQDGALFGSMNIYDNTAFPLREHTKKSESEIRKIVMEKLDLVGMPNDGHKFPGEISGGMRKRAGLARALVLDPE IILCDEPDSGLDPVRTAYLSQLLIDINAQIDATVLIVTHNINIARTVPDNMGMLFRKQLVMFGPREVLLTSEEPVVKQFL NGRRIGPIGMSEEKDEATAAAEQALVDAGQHDGGVEEIEGVPPQLQATPGMPERKAVARRKARVREILHTLPPAAQAAIL EELDRDQPQLSAPTTQTAATAPVENYDDSPTGVIEVPKQAGLSGQPPRSPSSGSSSNSLEVLFQGPTAAAAVSKGEELFT GVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMP EGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRH NIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGGGGENLYFQD YKDDDDKHHHHHH A0QS64 P42212 Conserved hypothetical integral membrane protein Yrbe1a Mycolicibacterium smegmatis MC2 155 0.027674618999999998 1 LEVO MTASTDGFVDYLRGQLEKPLATVGGFFKMSVMTGKALFTRPFQWKEFVLQSWFLIRVAFLPTLAVSIPLTVLIIFTLNIL LAEFGAADVSGAGAALGAVTQLGPLVTVLVVAGAGSTAICADLGARTVREEIDALEVLGIDPIERLVVPRVVASTFVAFM LNGAVITIGLVGGFFFGVYIQNVSAGAYVSTLTLLTGFPEVLISVVKATLFGMIAGLVGCYRGLTVAGGSKGVGTAVNET LVLCVVALFAVNVVLTTIGVRFGTGR I7F4Q4 ABC-transporter integral membrane protein Mycolicibacterium smegmatis MC2 155 0.030809025 1 LEVO MSTVQVLRSRFPRAFSRSSEIAATPARFLDSMGHVAWFVVQAIVHVPHAFRHYRRESLRLVAEIGMGTGAMAVIGGTVAI IGFVTLSAGSLIAIQGFASLGNIGVEAFTGFFAALANIRVVAPVVTGQALAATVGAGATAELGAMRISEEVDALEVMGIK SISYLVSTRIMAGAIVIIPLYAMAILLSFMSAQLVTTIFYSQSVGTYEHYFHTFLRVDDVMWSFLEVIIMSVIVMLNHCY FGYFASGGAVGVGEAVGRSMRTSLIAIVLVVLLASLALYGTDPNFNLTV A0QNR1 UNKNOWN LIGAND 31 UNL singleParticle particle 1.7 7.5 50.0 C4H13Cl2NO3 Tris-HCl 5.0 MgSO4 Magnesium sulfate 150.0 NaCl Sodium chloride 1.0 C24H46O11 n-dodecyl-beta-D-maltoside 1.0 C4H10O2S2 Dithiothreitol

50 mM Tris-HCl pH 7.5, 5 mM MgSO4, 150 mM NaCl, 1 mM DDM, 1 mM DTT

Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 2.0 ETHANE 100 295.15 FEI VITROBOT MARK IV

This sample contains a mixture of MCE proteins endogenously purified from Mycobacterium smegmatis.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 BIOQUANTUM (6k x 4k) 11520 8184 2 43925 2.0 60.0

Images were collected in super resolution mode.

1 2869223

Starting model was generated using cryoSPARC Ab initio Reconstruction.

C1 2.9 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 160443 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 4 85000.0 cryoSPARC 3.3.1

Consensus set of particles were 3D classified using cryoSPARC Heterogenous Refinement (four classes, a-d). Class c and d were combined to make Map2 (containing no density for LucB).

FLEXIBLE FIT

Model was initial fitted into the map using Chimera follow-by rigid body refinement in PHENIX. Models were further refined using PHENIX real-space refinement and then manually inspected in Coot.

Cross-correlation coefficient REAL emd_29024_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.7700188 1.2455974 0.00042125784 0.02100444 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Constituent Map2a used to in composite Map2. Map was generated by locally refining Class2 particles that were re-centered and extracted with a smaller boxsize (360 px). emd_29024_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.42858738 0.6768354 0.00038407426 0.050694518 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map B for Map2a emd_29024_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 528.32 528.32 528.32 90.0 90.0 90.0 X Y Z -0.40583476 0.7329653 0.00008751373 0.040667996 0.8255 0.8255 0.8255 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map A for raw map used as template to generate composite half map A. emd_29024_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 528.32 528.32 528.32 90.0 90.0 90.0 X Y Z -0.41501495 0.7039908 0.000093857794 0.040753283 0.8255 0.8255 0.8255 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map B for raw map used as template to generate composite half map B. emd_29024_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 528.32 528.32 528.32 90.0 90.0 90.0 X Y Z -0.451779 0.94361204 -0.000020415115 0.014326592 0.8255 0.8255 0.8255 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Raw map used as template to generate composite Map2. Map was generated by aligning Class2 particles that were re-extracted with a larger boxsize (640 px). emd_29024_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.42755198 0.66201174 0.0003758865 0.04993323 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map A for Map2a emd_29024_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.7086558 0.67293674 0.000718942 0.078634635 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map A for Map2b emd_29024_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.6516062 0.68583906 0.0007143891 0.07896379 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map B for Map2b emd_29024_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.73770493 1.1816484 0.000934531 0.027350478 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Constituent Map2b used to in composite Map2. Map was generated by locally refining Class2 particles that were re-centered and extracted with a smaller boxsize (360 px). emd_29024_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.6300363 0.63305545 0.00067939964 0.07628686 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map A for Map2c emd_29024_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.65140796 0.7127626 0.0006780299 0.07624982 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map B for Map2c emd_29024_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.7065672 1.147933 0.000792987 0.024536762 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Constituent Map2c used to in composite Map2. Map was generated by locally refining Class2 particles that were re-centered and extracted with a smaller boxsize (360 px). emd_29024_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.5463561 0.5892156 0.00034450646 0.06722704 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map A for Map2d emd_29024_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.58024997 0.6528725 0.00034455257 0.067618005 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Half map B for Map2d emd_29024_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.18 297.18 297.18 90.0 90.0 90.0 X Y Z -0.64683765 1.0216689 0.00054251374 0.019612884 0.82549995 0.82549995 0.82549995 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Constituent Map2d used to in composite Map2. Map was generated by locally refining Class2 particles that were re-centered and extracted with a smaller boxsize (360 px). emd_29024_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 528.32 528.32 528.32 90.0 90.0 90.0 Z Y X -9.153161000000001 13.010142999999999 -0.0013180847 0.99513704 0.8255 0.8255 0.8255 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Composite half map A for Map2 emd_29024_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 528.32 528.32 528.32 90.0 90.0 90.0 Z Y X -9.061809999999999 13.406383999999999 -0.0013617105 0.99493897 0.8255 0.8255 0.8255 AUTHOR ::::EMDATABANK.org::::EMD-29024:::: Composite half map B for Map2