[English] 日本語
Yorodumi
- EMDB-45399: Structure of the LPD-3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45399
TitleStructure of the LPD-3 complex
Map data
Sample
  • Complex: LPD-3 in complex with Spigot
    • 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
  • 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
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsClark SA / Kang Y
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45399.png

Downloads & links

-
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy SOFTWARE: 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 °

-
Supplemental data

-
Half map: #1

Fileemd_45399_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45399_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LPD-3 in complex with Spigot

EntireName: LPD-3 in complex with Spigot
Components
  • Complex: LPD-3 in complex with Spigot
    • 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
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEXADECANE

-
Supramolecule #1: LPD-3 in complex with Spigot

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

-
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: 483.883406 KDa
Recombinant expressionOrganism: Caenorhabditis elegans (invertebrata)
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 TAESFQTPRN EVKVFKPVVP NQYD LAVEW DEKVLDMTRD YEKHMQRMRT NKEDVVEKVK VMVNGSAMVS SIVLESVLND LYVSVTISQI VLAHSKNPMP DIPVV VHAV TLSTTPTAAA AEDKKTATLT KKSVSSTFKI DDLTVSLTKM KLTLSEADSS NKKSDILRCT LNSSSFNVHT NLKTLT SAK ESNRPKNNLI NSNIATTATL RLGALEGTMP MAAYSLHDVV MRHGKELEQQ LNRLAAQPAS TPLSSSTPFP SAEQSLL AK VADMKTAPEP VVITQAEFKP LTTLPATAAH VQDAKGQIVR RVPVAVVSFS IELTSIEMNI QLLPSLQAKY RINRATSN G ITGVQANWSI LLDEHFFEFC VTGQGGKTET FRLQLPSVTS DGLYQAEQGV SSQKPSTDKK LIYREGGSLQ MTVVLGRVN HIFTTELLNQ LMFAEHSFRT ELTALINRIR SSSFASTNSS RSAQSTNDRV NSTANLKLLL PVQTTSTPVH IEKPPLLFSI KIQTKEIPR KDEKTDKDAK TPKASGASGN LDQSQHPSHS THVKSTPWLQ LTAATPTQTA VRLTVDSLEG ELTNKWVVKE E GSKERIYG NAVIHFNAKL GQLIKPVPTG DSVAATDVTD LQEFATFMTQ VRVENKERNM FNSSYSYHIS LNRPIFLVKA AA IDKAILL WLNYKNTYDY WRNEREKVVQ EKTTTKLSNA GMFSPTQIAE DADMNLSLAI NNGMYMCMPL YSHDVTEGMP ALV LSLQKS NLSVLVKKEL TCKASFNGFK CSFVDDFDEQ ALTQSFLDAT HSDQSNCIFF PEGTYQLCSK AEATKGPAKW VLSV SAEMQ GVEIDLDTRI GKLAKLLVNT FSMIRTDDDD DMSFWGDEGE LDSDEEKVEG ASELKKLKAE EKVPWMENKM HEHSR AVFE LAARGVSNKL IEAEKHKLRQ YELIRFKAFR RNVVEKLKKG TTASRQHTET PPPQPRPDTT SRRNSRTTST SQKNSE DLT TPGDIETVNF NLDVKVNITS GTCTLRTQKK EGANQLALPG ILKRLNLGTK DIKAMFEPQI ITTTTFSIPS VEIKAYH VS DPSNRSTDEF CKDKREKISK GLAKDADKLH RDLHNKSRFG NTYINGGGGP KTSTVPPPPK RGCFYIFVGL ASMPSETV V TPHLATYFEQ VLEPLPPSAV FQSQNNTREA SVPDDGKGDA NNEVHNIMAM DTAAFPIDFV FYLDVQSSTI RFDGKQPTS RSQTQADCLL TLPRLTLELT SKRTRDNIDN YVGGIHISGQ FKGFMLKIYN PLELEPDSSR ALQLSLDLLS FVISRNKNSS TEPDNRVRF VFSSQISKAS FEYNFRRLGE LIQFPKPWYR AAIARRVFFG DQAAPRQKDD ASDITGTTRS RLPTDPKSLQ P PAASTAST GSGSFVPHQR KPWTALVLAA IQWNEFEVTA FMSNTMGKTT WKATKGLVWG DAKLNSLNER DVSISFVLGS SE LCARDGA ISGTIMLNNL KVSADHSLSA DVKRVPVNKA KIRLEWITAN IEWMSRRVLI AKWCGPSFKV NDYYKGLKEG DHF ALSELG MNVQASWKDL QVVITKSTVD DVAAIVNRLI SFIDEQLKNS RILLGNLSAS TNLKKQAQAL IESRKPTTHF WEKV LDYMS EMQMNEQLMG LMEREGAKVG GHIELKAGGI SLVMMKGDMN ADTWAVFHLR DACILFDPEA RMDFLDNSSQ QKIGI LLKQ TFCLQLGSRH GNQTENRANV CRVQTRFNNS RHLQKAEDIL EFFIGDVMKI IGSADHSEKK KLKEVEVIQS PISENE NTA KSPTSTFSRF RSPGTSKTKE SGPATNHNVM ELFQFPGLEA KMSSQQLNGV DDGDKYESVF QMPMDVLTTF VCDFFSE VA IETNFNAQVS FLPELLKSYL KESHSGTSSS HSTNSSPAVS SSKESVVSET SKDPRIFTCQ EWKVEPRVRF IDRIKWTP P VLDDILKKLQ IFDHRNTIPK VIQRAVLDPL DATLAASVIA TLQIVDNKKT IQKFKKSRTD SMAPTPKRRD SRRSSEEVS VSIDIPDIIT DISDASFRPK HNGSGVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK LICTTGKLPV PWPTLVTTL GYGLMCFARY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDTLVNRIE LKGIDFKEDG N ILGHKLEY NYNSHNVYIT ADKQKNGIKA NFKIRHNIED GGVQLADHYQ QNTPIGDGPV LLPDNHYLSY QSKLSKDPNE KR DHMVLLE FVTAAGITLG MDELYKGSGL EVLFQGPANS GVDYKDHDGD YKDHDIDYKD DDDK

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

-
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

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

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 18 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

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

-
Macromolecule #4: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 4 / Number of copies: 12 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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 / Number images used: 285377
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more