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- EMDB-45399: Structure of the LPD-3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45399
TitleStructure of the LPD-3 complex
Map data
Sample
  • Complex: LPD-3 complex
    • Protein or peptide: Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
    • Protein or peptide: Defect at low temperature protein 1
  • Protein or peptide: Vesicle transport protein
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEXADECANE
KeywordsNative / membrane protein complex / BLTP / LIPID TRANSPORT
Function / homology
Function and homology information


synaptic vesicle endocytosis / presynapse / membrane
Similarity search - Function
Transmembrane protein 170 / Putative transmembrane protein 170 / C1orf43 / Protein KIAA1109 / : / : / : / NICE-3 protein / BLTP1-like family N-terminal region / BLTP1-like family middle region ...Transmembrane protein 170 / Putative transmembrane protein 170 / C1orf43 / Protein KIAA1109 / : / : / : / NICE-3 protein / BLTP1-like family N-terminal region / BLTP1-like family middle region / BLTP1-like family C-terminal region / Fragile site-associated protein C-terminus
Similarity search - Domain/homology
Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein / Defect at low temperature protein 1 / Vesicle transport protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsClark SA / Vanni S / Kang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Nature / Year: 2025
Title: Structural basis of lipid transfer by a bridge-like lipid-transfer protein.
Authors: Yunsik Kang / Katherine S Lehmann / Hannah Long / Amanda Jefferson / Maria Purice / Marc Freeman / Sarah Clark /
Abstract: Bridge-like lipid-transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane-contact sites and are thought to mediate the bulk transfer of lipids from a ...Bridge-like lipid-transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane-contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum, to an acceptor membrane, such as that of the cell or an organelle. Although BLTPs are fundamentally important for a wide array of cellular functions, their architecture, composition and lipid-transfer mechanisms remain poorly characterized. Here we present the subunit composition and the cryogenic electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic Caenorhabditis elegans. LPD-3 folds into an elongated, rod-shaped tunnel of which the interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, one of which we have named Spigot and the other of which remains unnamed. Spigot interacts with the N-terminal end of LPD-3 where lipids are expected to enter the tunnel, and experiments in multiple model systems indicate that Spigot has a conserved role in BLTP function. Our LPD-3 complex structural data reveal protein-lipid interactions that suggest a model for how the native LPD-3 complex mediates bulk lipid transport and provides a foundation for mechanistic studies of BLTPs.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2025
Title: TMEM170 proteins are lipid scramblases associated with bridge-type lipid transporters BLTP1/Csf1
Authors: Rocha-Roa C / Chandran Blair P / Sidhu G / Alvarez D / Davey M / Conibear E / Vanni S
History
DepositionJun 17, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45399.png

Downloads & links

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Map

FileDownload / File: emd_45399.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 756 pix.
= 595.728 Å		0.79 Å/pix.
x 756 pix.
= 595.728 Å		0.79 Å/pix.
x 756 pix.
= 595.728 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.31038254 - 0.7124187
Average (Standard dev.)0.000013521269 (±0.007400532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions756756756
Spacing756756756
CellA=B=C: 595.72797 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45399_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45399_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LPD-3 complex

EntireName: LPD-3 complex
Components
  • Complex: LPD-3 complex
    • Protein or peptide: Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
    • Protein or peptide: Defect at low temperature protein 1
  • Protein or peptide: Vesicle transport protein
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEXADECANE

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Supramolecule #1: LPD-3 complex

SupramoleculeName: LPD-3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Bridge-like lipid transfer protein family member 1 C-terminal dom...

MacromoleculeName: Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 483.608094 KDa
SequenceString: MSDFDIQIKI DDAQLDLKGV SFWVTASVVT LFLAWSTFVV LFFSRVSALF FTFVIDKYLR LSKNGIHFKI GGISISGLHA GKIMFRNVI YDNGDMTIKV NDGHLLFKYW KSVEHRHLNL STKRASRLHL VLNGLHVNIY NNLTKYTEIA RIRRFDWFFE N TNMNDARR ...String:
MSDFDIQIKI DDAQLDLKGV SFWVTASVVT LFLAWSTFVV LFFSRVSALF FTFVIDKYLR LSKNGIHFKI GGISISGLHA GKIMFRNVI YDNGDMTIKV NDGHLLFKYW KSVEHRHLNL STKRASRLHL VLNGLHVNIY NNLTKYTEIA RIRRFDWFFE N TNMNDARR PQTKPPDTCR SPPSSVWENM WNLLGIVHIE VSAGCILVGN KFLPYALWTR FENLNSKTSV TESANDRALL TF EGETENV AVSLIKNEQF DFTAKDKDPP RTMGNDGCPL LQSASLEFVY KQDLLGYVTD DEPQSITLKL PLWSSEWRFG NNT VLSYGP WAEQQRFLIY SFFYPPDFQN STATAMPTRG KKRIHVKHDV KIILTKETCM DIWFMRGEQL ESIRTRCGPL SSLD MSILW ITTEKGFYWN MKAEFLNFEA TTSLIFTKLF SCKKFNVDGS FVYPLTWNGE QTWTIDYAFT KANAWFVWDH KRLFT DLIN DWIGDDPSDI SKFVPFRVHN RMKVVDGFEV IMLLNESNWV DTADMNAENV EVAIVGEKLS FECELPFVDF LPQTQM VKY EMRGEKSVAM RAKFPPDSAT APIRAALSRL ARCNSYAPPS KHGTHSLDTD VWFELWRTEL VKMDFDHHYR PLIVKSN IP SDIPFSILSD YLPPPANHPW DLEPDYLGVD ILIEGSDVKF TGLLVKLLFE LKNNYFGWYD SMTSVDDEKI DDPIKLKA S FDKTNANGMK PVEYFRTMNV DVTVRVCNVR AEMLLYSPAI DEGAEPEKVP VVFVEEVAVE VKKTKTQALI QVGVSPACA YLDKSSQGSG PGCITLSGFQ FRGHAMYSAK EVAWNMGLVE YGWIMEILVG DIAGTLDFPA HAHVLHQIME SLLMFVISPD DATKVPDRM QFCQHGQLIK ACSIAGKKTN EILGPCKTEE QMKYRQIRIS VDSVNLTFVE EKTILQISAD PVRVTICNAH E SRFTEHVC IRVPGISIRQ AVRIKEKPEN IWIEGANAAI EGVSLDIELP TPKSASPTIG KERLEFVRMH DADTKRLHFL WA DHSVWGC ACFGNTCFFG DVDEIGSTFM ETLTKKKFFV PGIERNPEKQ PQVMQSVILK NKPILSNQPH MFYKKPKNAD VVI TIRKES TGDTESFHSA RSQQSPGLRI LQSMEMSSSY ATFVDNVRVE LPSAITVPQF GEPGAILEWC QAHQATRIIN DVNT SGVNE VRFLSKPKKS QDIEYNTSRD TLGKRRLAIN GVAATSLDLF VTPIGIEAFE RLVTAASHSV PAINPCILVH MCYRD CVLK KHRQPLTESL FADEDNDSEP ISEVDITVDL PRVSIGLFQC GVKKNIVKSN HTDHITANMG LLLIDRAFIQ SKLIPA ESV SQDFSADTSN LSSTLYQLNG SAITVQLLQL TNRDAPDFGS SGTATTPNNW EHCAISRRMN NLEPRVMMDF NVSDTLI IL ERRPIILLLP DKSTTAITPI HSPANAPTPT AMNRTPTLTL TPSAGAGGGE RAEPMRKKKK MICEHYLKAD IGSVTTAL V MARPQELTAG DEFPIYEALA PVMVSWLSVV ENFLRTVDKF IHTVECWKSV AMAKVLKLAL DSTDEKVVVK VGKNRMGRT RVLSAHQASC PSCILLKTLF RWFAYAGNAP GAINHRLDIR PEFEIEETRK TALMALLSHW QSDVGKELKL VSYEDAHRFK VTRPDEAAI VALTKSKRLK RKMLEKKESS KKETRVVMEV KPEQPKAKRG RMSPAPLLKK LRKKAGDDDF DDDSMKFLSD V EMQEFNTL PLYEDYEDDE MLENLDSEPK IDDKVDLYTW MRNAQRESTL RRRKLAGGAE GSVKDDLNLK GYINPMDIQQ KA YYYNIYR WAQLQWTSLD GIEKDHWHLD YSVTLREVDV RMMAKSIKNS SDHLRQYITP AQQKVMQVRN AAVNGGMVWK MER DERRKI PLHGQWNISY SGNVEGIRFL IGMATVSLGK ELSLVLRVAM EAKNELRMHS TAESTPRNEV KVFKPVVPNQ YDLA VEWDE KVLDMTRDYE KHMQRMRTNK EDVVEKVKVM VNGSAMVSSI VLESVLNDLY VSVTISQIVL AHSKNPMPDI PVVVH AVTL STTPTAAAAE DKKTATLTKK SVSSTFKIDD LTVSLTKMKL TLSEADSSNK KSDILRCTLN SSSFNVHTNL KTLTSA KES NRPKNNLINS NIATTATLRL GALEGTMPMA AYSLHDVVMR HGKELEQQLN RLAAQPASTP LSSSTPFPSA EQSLLAK VA DMKTAPEPVV ITQAEFKPLT TLPATAAHVQ DAKGQIVRRV PVAVVSFSIE LTSIEMNIQL LPSLQAKYRI NRATSNGI T GVQANWSILL DEHFFEFCVT GQGGKTETFR LQLPSVTSDG LYQAEQGVSS QKPSTDKKLI YREGGSLQMT VVLGRVNHI FTTELLNQLM FAEHSFRTEL TALINRIRSS SFASTNSSRS AQSTNDRVNS TANLKLLLPV QTTSTPVHIE KPPLLFSIKI QTKEIPRKD EKTDKDAKTP KASGASGNLD QSQHPSHSTH VKSTPWLQLT AATPTQTAVR LTVDSLEGEL TNKWVVKEEG S KERIYGNA VIHFNAKLGQ LIKPVPTGDS VAATDVTDLQ EFATFMTQVR VENKERNMFN SSYSYHISLN RPIFLVKAAA ID KAILLWL NYKNTYDYWR NEREKVVQEK TTTKLSNAGM FSPTQIAEDA DMNLSLAINN GMYMCMPLYS HDVTEGMPAL VLS LQKSNL SVLVKKELTC KASFNGFKCS FVDDFDEQAL TQSFLDATHS DQSNCIFFPE GTYQLCSKAE ATKGPAKWVL SVSA EMQGV EIDLDTRIGK LAKLLVNTFS MIRTDDDDDM SFWGDEGELD SDEEKVEGAS ELKKLKAEEK VPWMENKMHE HSRAV FELA ARGVSNKLIE AEKHKLRQYE LIRFKAFRRN VVEKLKKGTT ASRQHTETPP PQPRPDTTSR RNSRTTSTSQ KNSEDL TTP GDIETVNFNL DVKVNITSGT CTLRTQKKEG ANQLALPGIL KRLNLGTKDI KAMFEPQIIT TTTFSIPSVE IKAYHVS DP SNRSTDEFCK DKREKISKGL AKDADKLHRD LHNKSRFGNT YINGGGGPKT STVPPPPKRG CFYIFVGLAS MPSETVVT P HLATYFEQVL EPLPPSAVFQ SQNNTREASV PDDGKGDANN EVHNIMAMDT AAFPIDFVFY LDVQSSTIRF DGKQPTSRS QTQADCLLTL PRLTLELTSK RTRDNIDNYV GGIHISGQFK GFMLKIYNPL ELEPDSSRAL QLSLDLLSFV ISRNKNSSTE PDNRVRFVF SSQISKASFE YNFRRLGELI QFPKPWYRAA IARRVFFGDQ AAPRQKDDAS DITGTTRSRL PTDPKSLQPP A ASTASTGS GSFVPHQRKP WTALVLAAIQ WNEFEVTAFM SNTMGKTTWK ATKGLVWGDA KLNSLNERDV SISFVLGSSE LC ARDGAIS GTIMLNNLKV SADHSLSADV KRVPVNKAKI RLEWITANIE WMSRRVLIAK WCGPSFKVND YYKGLKEGDH FAL SELGMN VQASWKDLQV VITKSTVDDV AAIVNRLISF IDEQLKNSRI LLGNLSASTN LKKQAQALIE SRKPTTHFWE KVLD YMSEM QMNEQLMGLM EREGAKVGGH IELKAGGISL VMMKGDMNAD TWAVFHLRDA CILFDPEARM DFLDNSSQQK IGILL KQTF CLQLGSRHGN QTENRANVCR VQTRFNNSRH LQKAEDILEF FIGDVMKIIG SADHSEKKKL KEVEVIQSPI SENENT AKS PTSTFSRFRS PGTSKTKESG PATNHNVMEL FQFPGLEAKM SSQQLNGVDD GDKYESVFQM PMDVLTTFVC DFFSEVA IE TNFNAQVSFL PELLKSYLKE SHSGTSSSHS TNSSPAVSSS KESVVSETSK DPRIFTCQEW KVEPRVRFID RIKWTPPV L DDILKKLQIF DHRNTIPKVI QRAVLDPLDA TLAASVIATL QIVDNKKTIQ KFKKSRTDSM APTPKRRDSR RSSEEVSVS IDIPDIITDI SDASFRPKHN GSGVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKLI CTTGKLPVPW PTLVTTLGY GLMCFARYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI L GHKLEYNY NSHNVYITAD KQKNGIKANF KIRHNIEDGG VQLADHYQQN TPIGDGPVLL PDNHYLSYQS KLSKDPNEKR DH MVLLEFV TAAGITLGMD ELYKGSGLEV LFQGPANSGV DYKDHDGDYK DHDIDYKDDD DK

UniProtKB: Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein

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Macromolecule #2: Defect at low temperature protein 1

MacromoleculeName: Defect at low temperature protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 31.56448 KDa
SequenceString: MRIFVFDGTS VIYVCAVIIL ILIWVAIIGQ RQIWRHRHNV ARVRPQVSLS SRISSKKAVL LRETQLDTVM RLRCENQARL TDCISLQFH GEKPYVHRMI AVDEVTLEID GQLNRIEGAV QRQAGESTYS YLKRIREKVP SIPLNLVHRI AFLQESARFR P EKFDVEQV ...String:
MRIFVFDGTS VIYVCAVIIL ILIWVAIIGQ RQIWRHRHNV ARVRPQVSLS SRISSKKAVL LRETQLDTVM RLRCENQARL TDCISLQFH GEKPYVHRMI AVDEVTLEID GQLNRIEGAV QRQAGESTYS YLKRIREKVP SIPLNLVHRI AFLQESARFR P EKFDVEQV MELRSLLNQF LRILSAEYDS LSDEPDMAAP RGVIASFYQF GQKIMPNNSG SKRRRNKFGG SDGVRLLMKE RE EQLSLLS PLARASADSP APAAHLRRQS DSHSALLPQ

UniProtKB: Defect at low temperature protein 1

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Macromolecule #3: Vesicle transport protein

MacromoleculeName: Vesicle transport protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 16.205293 KDa
SequenceString:
MPENKEIITI FENSRNYTNL TSESTYSLAG ALLLSGKYMN DWWEITLSIF LWMSLSFMVI SLGATILSLF TLRKHPYVCF IPIPFIIMM FIIPFVFGAP TSMVLALAMY ASKNAVSTWY CAIMGIIQTL LIFVTSVTRI HATL

UniProtKB: Vesicle transport protein

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Macromolecule #4: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 4 / Number of copies: 18 / Formula: PEE
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #5: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 5 / Number of copies: 12 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 285377
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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