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- PDB-9cap: Structure of the LPD-3 complex -

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Basic information

Entry
Database: PDB / ID: 9cap
TitleStructure of the LPD-3 complex
Components
  • Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
  • Defect at low temperature protein 1
KeywordsLIPID TRANSPORT / Native / membrane protein complex / BLTP
Function / homology
Function and homology information


synaptic vesicle endocytosis / presynapse / membrane
Similarity search - Function
C1orf43 / Fragile site-associated protein, C-terminal / Protein KIAA1109 / : / NICE-3 protein / : / BLTP1-like family N-terminal region / Fragile site-associated protein C-terminus
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / HEXADECANE / Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein / Defect at low temperature protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsClark, S.A. / Kang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
B: Defect at low temperature protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,55832
Polymers515,4482
Non-polymers16,11030
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 483883.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lpd-3, CELE_Y47G6A.23, Y47G6A.23 / Production host: Caenorhabditis elegans (invertebrata) / References: UniProt: A0A0K3AWP8
#2: Protein Defect at low temperature protein 1


Mass: 31564.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q4W5H0
#3: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LPD-3 in complex with Spigot / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285377 / Symmetry type: POINT

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