Intermembrane lipid transport complex LetAB from Escherichia coli (Crosslinked, Composite Map 1)

2026-04-01 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2025-02-10 2025-07-16 2025-07-16 2026-04-01 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM128777 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1K99GM157496-01 United States Other private The Charles H. Revson Foundation Intermembrane lipid transport complex LetAB from Escherichia coli (Crosslinked, Composite Map 1) Santarossa CC Bhabha G Ekiert DC Lipid transporter, Outer membrane integrity, MCE system, Metal-binding protein, Intermembrane complex, LIPID TRANSPORT Santarossa CC Li Y Yousef S Hasdemir HS Rodriguez CC Haase MAB Baek M Coudray N Pavek JG Focke KN Silverberg AL Bautista C Yeh JT Marty MT Baker D Tajkhorshid E Ekiert DC Bhabha G LetA defines a structurally distinct transporter family. Nature UK 651 1097 1106 2026 41565823 doi:10.1038/s41586-025-09990-0 1476-4687 0006 NATUAS EMD-49145 focused EM volume

Local refinement of crosslinked LetA and LetB MCE Rings 1 and 2 (Map 1a)

EMD-49146 focused EM volume

Local refinement of crosslinked LetB MCE Rings 2, 3 and 4 (Map 1b)

EMD-49147 focused EM volume

Local refinement of crosslinked LetB MCE Rings 5, 6 and 7 (Map 1c)

9n8w FULLOVERLAP EMDB EMD-49145 focused EM volume

Local refinement of crosslinked LetA and LetB MCE Rings 1 and 2 (Map 1a)

EMDB EMD-49146 focused EM volume

Local refinement of crosslinked LetB MCE Rings 2, 3 and 4 (Map 1b)

EMDB EMD-49147 focused EM volume

Local refinement of crosslinked LetB MCE Rings 5, 6 and 7 (Map 1c)

EMDB EMD-49148 associated EM volume

Intermembrane lipid transport complex LetAB from Escherichia coli (Crosslinked, Composite model corresponding to Map 1)

LetAB complex crosslinked with glutaraldehyde LetAB complex crosslinked with glutaraldehyde 0 1 2 Escherichia coli MG1655 0.618 Intermembrane transport protein YebS Escherichia coli str. K-12 substr. MG1655 0.050667746 1 Escherichia coli B LEVO MHHHHHHQHQHENLYFQGMALNTPQITPTKKITVRAIGEELPRGDYQRCPQCDMLFSLPEINSHQSAYCPRCQAKIRDGR DWSLTRLAAMAFTMLLLMPFAWGEPLLHIWLLGIRIDANVMQGIWQMTKQGDAITGSMVFFCVIGAPLILVTSIAYLWFG NRLGMNLRPVLLMLERLKEWVMLDIYLVGIGVASIKVQDYAHIQAGVGLFSFVALVILTTVTLSHLNVEELWERFYPQRP ATRRDEKLRVCLGCHFTGYPDQRGRCPRCHIPLRLRRRHSLQKCWAALLASIVLLLPANLLPISIIYLNGGRQEDTILSG IMSLASSNIAVAGIVFIASILVPFTKVIVMFTLLLSIHFKCQQGLRTRILLLRMVTWIGRWSMLDLFVISLTMSLINRDQ ILAFTMGPAAFYFGAAVILTILAVEWLDSRLLWDAHESGNARFDD P0AD03 Intermembrane transport protein YebT Escherichia coli str. K-12 substr. MG1655 0.09507221099999999 6 Escherichia coli LEVO MSQETPASTTEAQIKNKRRISPFWLLPFIALMIASWLIWDSYQDRGNTVTIDFMSADGIVPGRTPVRYQGVEVGTVQDIS LSDDLRKIEVKVSIKSDMKDALREETQFWLVTPKASLAGVSGLDALVGGNYIGMMPGKGKEQDHFVALDTQPKYRLDNGD LMIHLQAPDLGSLNSGSLVYFRKIPVGKVYDYAINPNKQGVVIDVLIERRFTDLVKKGSRFWNVSGVDANVSISGAKVKL ESLAALVNGAIAFDSPEESKPAEAEDTFGLYEDLAHSQRGVIIKLELPSGAGLTADSTPLMYQGLEVGQLTKLDLNPGGK VTGEMTVDPSVVTLLRENTRIELRNPKLSLSDANLSALLTGKTFELVPGDGEPRKEFVVVPGEKALLHEPDVLTLTLTAP ESYGIDAGQPLILHGVQVGQVIDRKLTSKGVTFTVAIEPQHRELVKGDSKFVVNSRVDVKVGLDGVEFLGASASEWINGG IRILPGDKGEMKASYPLYANLEKALENSLSDLPTTTVSLSAETLPDVQAGSVVLYRKFEVGEVITVRPRANAFDIDLHIK PEYRNLLTSNSVFWAEGGAKVQLNGSGLTVQASPLSRALKGAISFDNLSGASASQRKGDKRILYASETAARAVGGQITLH AFDAGKLAVGMPIRYLGIDIGQIQTLDLITARNEVQAKAVLYPEYVQTFARGGTRFSVVTPQISAAGVEHLDTILQPYIN VEPGRGNPRRDFELQEATITDSRYLDGLSIIVEAPEAGSLGIGTPVLFRGLEVGTVTGMTLGTLSDRVMIAMRISKRYQH LVRNNSVFWLASGYSLDFGLTGGVVKTGTFNQFIRGGIAFATPPGTPLAPKAQEGKHFLLQESEPKEWREWGTALPK P76272 ZINC ION 6.5409e-05 2 ZN singleParticle particle 1 8.0 20.0 Tris-HCl tris(hydroxymethyl)aminomethane hydrochloride 150.0 NaCl sodium chloride 0.5 DDM n-Dodecyl-B-D-maltoside Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE 5 ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 0.1 2.1 4.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOCONTINUUM (6k x 4k) 1 12464 50.0 1 3582925

Particles were selected by template-based auto-picking in cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.5 FSC 0.143 CUT-OFF 158666 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_49148.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 370.386 370.386 370.386 90.0 90.0 90.0 Z Y X -10.027485 23.27833 0.015748618 0.6178917 1.02885 1.02885 1.02885 2.25 AUTHOR ::::EMDATABANK.org::::EMD-49148:::: 6V0J PDB experimental model

The initial model consisted of the complete biological assembly for PDB entry 6V0J

6V0F PDB experimental model

The initial model consisted of the complete biological assembly for PDB entry 6V0F

6V0E PDB experimental model

The initial model consisted of the complete biological assembly for PDB entry 6V0E

LetA RoseTTAFold in silico model

The initial model consisted of the complete biological assembly for RoseTTAFold LetA

FLEXIBLE FIT

Model was fit as a rigid-body into the individual map using Chimera. Real space refinement was carried out in PHENIX. Models were then manually inspected and adjusted in Coot. Iterative rounds of model building and refinement were performed.

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