[English] 日本語
Yorodumi
- EMDB-45276: Map of full-length LPD-3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45276
TitleMap of full-length LPD-3 complex
Map data
Sample
  • Complex: Complex of LPD-3 with auxiliary proteins Spigot and Intake
    • Protein or peptide: LPD-3
    • Protein or peptide: Spigot
    • Protein or peptide: Intake
KeywordsNative membrane 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 / Uncharacterized protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsClark SA / Kang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded 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 10, 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_45276.png

Downloads & links

-
Map

FileDownload / File: emd_45276.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 512 pix.
= 806.912 Å		1.58 Å/pix.
x 512 pix.
= 806.912 Å		1.58 Å/pix.
x 512 pix.
= 806.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.576 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3219864 - 0.6007063
Average (Standard dev.)0.000066624256 (±0.009022662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 806.912 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_45276_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45276_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of LPD-3 with auxiliary proteins Spigot and Intake

EntireName: Complex of LPD-3 with auxiliary proteins Spigot and Intake
Components
  • Complex: Complex of LPD-3 with auxiliary proteins Spigot and Intake
    • Protein or peptide: LPD-3
    • Protein or peptide: Spigot
    • Protein or peptide: Intake

-
Supramolecule #1: Complex of LPD-3 with auxiliary proteins Spigot and Intake

SupramoleculeName: Complex of LPD-3 with auxiliary proteins Spigot and Intake
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

-
Macromolecule #1: LPD-3

MacromoleculeName: LPD-3 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MSDFDIQIKI DDAQLDLKGV SFWVTASVVT LFLAWSTFVV LFFSRVSALF FTFVIDKYLR LSKNGIHFKI GGISISGLHA GKIMFRNVIY DNGDMTIKVN DGHLLFKYWK SVEHRHLNLS TKRASRLHLV LNGLHVNIYN NLTKYTEIAR IRRFDWFFEN TNMNDARRPQ ...String:
MSDFDIQIKI DDAQLDLKGV SFWVTASVVT LFLAWSTFVV LFFSRVSALF FTFVIDKYLR LSKNGIHFKI GGISISGLHA GKIMFRNVIY DNGDMTIKVN DGHLLFKYWK SVEHRHLNLS TKRASRLHLV LNGLHVNIYN NLTKYTEIAR IRRFDWFFEN TNMNDARRPQ TKPPDTCRSP PSSVWENMWN LLGIVHIEVS AGCILVGNKF LPYALWTRFE NLNSKTSVTE SANDRALLTF EGETENVAVS LIKNEQFDFT AKDKDPPRTM GNDGCPLLQS ASLEFVYKQD LLGYVTDDEP QSITLKLPLW SSEWRFGNNT VLSYGPWAEQ QRFLIYSFFY PPDFQNSTAT AMPTRGKKRI HVKHDVKIIL TKETCMDIWF MRGEQLESIR TRCGPLSSLD MSILWITTEK GFYWNMKAEF LNFEATTSLI FTKLFSCKKF NVDGSFVYPL TWNGEQTWTI DYAFTKANAW FVWDHKRLFT DLINDWIGDD PSDISKFVPF RVHNRMKVVD GFEVIMLLNE SNWVDTADMN AENVEVAIVG EKLSFECELP FVDFLPQTQM VKYEMRGEKS VAMRAKFPPD SATAPIRAAL SRLARCNSYA PPSKHGTHSL DTDVWFELWR TELVKMDFDH HYRPLIVKSN IPSDIPFSIL SDYLPPPANH PWDLEPDYLG VDILIEGSDV KFTGLLVKLL FELKNNYFGW YDSMTSVDDE KIDDPIKLKA SFDKTNANGM KPVEYFRTMN VDVTVRVCNV RAEMLLYSPA IDEGAEPEKV PVVFVEEVAV EVKKTKTQAL IQVGVSPACA YLDKSSQGSG PGCITLSGFQ FRGHAMYSAK EVAWNMGLVE YGWIMEILVG DIAGTLDFPA HAHVLHQIME SLLMFVISPD DATKVPDRMQ FCQHGQLIKA CSIAGKKTNE ILGPCKTEEQ MKYRQIRISV DSVNLTFVEE KTILQISADP VRVTICNAHE SRFTEHVCIR VPGISIRQAV RIKEKPENIW IEGANAAIEG VSLDIELPTP KSASPTIGKE RLEFVRMHDA DTKRLHFLWA DHSVWGCACF GNTCFFGDVD EIGSTFMETL TKKKFFVPGI ERNPEKQPQV MQSVILKNKP ILSNQPHMFY KKPKNADVVI TIRKESTGDT ESFHSARSQQ SPGLRILQSM EMSSSYATFV DNVRVELPSA ITVPQFGEPG AILEWCQAHQ ATRIINDVNT SGVNEVRFLS KPKKSQDIEY NTSRDTLGKR RLAINGVAAT SLDLFVTPIG IEAFERLVTA ASHSVPAINP CILVHMCYRD CVLKKHRQPL TESLFADEDN DSEPISEVDI TVDLPRVSIG LFQCGVKKNI VKSNHTDHIT ANMGLLLIDR AFIQSKLIPA ESVSQDFSAD TSNLSSTLYQ LNGSAITVQL LQLTNRDAPD FGSSGTATTP NNWEHCAISR RMNNLEPRVM MDFNVSDTLI ILERRPIILL LPDKSTTAIT PIHSPANAPT PTAMNRTPTL TLTPSAGAGG GERAEPMRKK KKMICEHYLK ADIGSVTTAL VMARPQELTA GDEFPIYEAL APVMVSWLSV VENFLRTVDK FIHTVECWKS VAMAKVLKLA LDSTDEKVVV KVGKNRMGRT RVLSAHQASC PSCILLKTLF RWFAYAGNAP GAINHRLDIR PEFEIEETRK TALMALLSHW QSDVGKELKL VSYEDAHRFK VTRPDEAAIV ALTKSKRLKR KMLEKKESSK KETRVVMEVK PEQPKAKRGR MSPAPLLKKL RKKAGDDDFD DDSMKFLSDV EMQEFNTLPL YEDYEDDEML ENLDSEPKID DKVDLYTWMR NAQRESTLRR RKLAGGAEGS VKDDLNLKGY INPMDIQQKA YYYNIYRWAQ LQWTSLDGIE KDHWHLDYSV TLREVDVRMM AKSIKNSSDH LRQYITPAQQ KVMQVRNAAV NGGMVWKMER DERRKIPLHG QWNISYSGNV EGIRFLIGMA TVSLGKELSL VLRVAMEAKN ELRMHSTAES FQTPRNEVKV FKPVVPNQYD LAVEWDEKVL DMTRDYEKHM QRMRTNKEDV VEKVKVMVNG SAMVSSIVLE SVLNDLYVSV TISQIVLAHS KNPMPDIPVV VHAVTLSTTP TAAAAEDKKT ATLTKKSVSS TFKIDDLTVS LTKMKLTLSE ADSSNKKSDI LRCTLNSSSF NVHTNLKTLT SAKESNRPKN NLINSNIATT ATLRLGALEG TMPMAAYSLH DVVMRHGKEL EQQLNRLAAQ PASTPLSSST PFPSAEQSLL AKVADMKTAP EPVVITQAEF KPLTTLPATA AHVQDAKGQI VRRVPVAVVS FSIELTSIEM NIQLLPSLQA KYRINRATSN GITGVQANWS ILLDEHFFEF CVTGQGGKTE TFRLQLPSVT SDGLYQAEQG VSSQKPSTDK KLIYREGGSL QMTVVLGRVN HIFTTELLNQ LMFAEHSFRT ELTALINRIR SSSFASTNSS RSAQSTNDRV NSTANLKLLL PVQTTSTPVH IEKPPLLFSI KIQTKEIPRK DEKTDKDAKT PKASGASGNL DQSQHPSHST HVKSTPWLQL TAATPTQTAV RLTVDSLEGE LTNKWVVKEE GSKERIYGNA VIHFNAKLGQ LIKPVPTGDS VAATDVTDLQ EFATFMTQVR VENKERNMFN SSYSYHISLN RPIFLVKAAA IDKAILLWLN YKNTYDYWRN EREKVVQEKT TTKLSNAGMF SPTQIAEDAD MNLSLAINNG MYMCMPLYSH DVTEGMPALV LSLQKSNLSV LVKKELTCKA SFNGFKCSFV DDFDEQALTQ SFLDATHSDQ SNCIFFPEGT YQLCSKAEAT KGPAKWVLSV SAEMQGVEID LDTRIGKLAK LLVNTFSMIR TDDDDDMSFW GDEGELDSDE EKVEGASELK KLKAEEKVPW MENKMHEHSR AVFELAARGV SNKLIEAEKH KLRQYELIRF KAFRRNVVEK LKKGTTASRQ HTETPPPQPR PDTTSRRNSR TTSTSQKNSE DLTTPGDIET VNFNLDVKVN ITSGTCTLRT QKKEGANQLA LPGILKRLNL GTKDIKAMFE PQIITTTTFS IPSVEIKAYH VSDPSNRSTD EFCKDKREKI SKGLAKDADK LHRDLHNKSR FGNTYINGGG GPKTSTVPPP PKRGCFYIFV GLASMPSETV VTPHLATYFE QVLEPLPPSA VFQSQNNTRE ASVPDDGKGD ANNEVHNIMA MDTAAFPIDF VFYLDVQSST IRFDGKQPTS RSQTQADCLL TLPRLTLELT SKRTRDNIDN YVGGIHISGQ FKGFMLKIYN PLELEPDSSR ALQLSLDLLS FVISRNKNSS TEPDNRVRFV FSSQISKASF EYNFRRLGEL IQFPKPWYRA AIARRVFFGD QAAPRQKDDA SDITGTTRSR LPTDPKSLQP PAASTASTGS GSFVPHQRKP WTALVLAAIQ WNEFEVTAFM SNTMGKTTWK ATKGLVWGDA KLNSLNERDV SISFVLGSSE LCARDGAISG TIMLNNLKVS ADHSLSADVK RVPVNKAKIR LEWITANIEW MSRRVLIAKW CGPSFKVNDY YKGLKEGDHF ALSELGMNVQ ASWKDLQVVI TKSTVDDVAA IVNRLISFID EQLKNSRILL GNLSASTNLK KQAQALIESR KPTTHFWEKV LDYMSEMQMN EQLMGLMERE GAKVGGHIEL KAGGISLVMM KGDMNADTWA VFHLRDACIL FDPEARMDFL DNSSQQKIGI LLKQTFCLQL GSRHGNQTEN RANVCRVQTR FNNSRHLQKA EDILEFFIGD VMKIIGSADH SEKKKLKEVE VIQSPISENE NTAKSPTSTF SRFRSPGTSK TKESGPATNH NVMELFQFPG LEAKMSSQQL NGVDDGDKYE SVFQMPMDVL TTFVCDFFSE VAIETNFNAQ VSFLPELLKS YLKESHSGTS SSHSTNSSPA VSSSKESVVS ETSKDPRIFT CQEWKVEPRV RFIDRIKWTP PVLDDILKKL QIFDHRNTIP KVIQRAVLDP LDATLAASVI ATLQIVDNKK TIQKFKKSRT DSMAPTPKRR DSRRSSEEVS VSIDIPDIIT DISDASFRPK HN

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

-
Macromolecule #2: Spigot

MacromoleculeName: Spigot / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MRIFVFDGTS VIYVCAVIIL ILIWVAIIGQ RQIWRHRHNV ARVRPQVSLS SRISSKKAVL LRETQLDTVM RLRCENQARL TDCISLQFHG EKPYVHRMIA VDEVTLEIDG QLNRIEGAVQ RQAGESTYSY LKRIREKVPS IPLNLVHRIA FLQESARFRP EKFDVEQVME ...String:
MRIFVFDGTS VIYVCAVIIL ILIWVAIIGQ RQIWRHRHNV ARVRPQVSLS SRISSKKAVL LRETQLDTVM RLRCENQARL TDCISLQFHG EKPYVHRMIA VDEVTLEIDG QLNRIEGAVQ RQAGESTYSY LKRIREKVPS IPLNLVHRIA FLQESARFRP EKFDVEQVME LRSLLNQFLR ILSAEYDSLS DEPDMAAPRG VIASFYQFGQ KIMPNNSGSK RRRNKFGGSD GVRLLMKERE EQLSLLSPLA RASADSPAPA AHLRRQSDSH SALLPQ

UniProtKB: Defect at low temperature protein 1

-
Macromolecule #3: Intake

MacromoleculeName: Intake / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MSRDVSLSPK SGDIRFNGTE PPVKVEVVDE EQSSLNNQLG FSTTLSTSFV LSEDLSESID DLTVTSKDKK KLRPSKVAED IGRKRKDTTN SITNFFHRFT RGDREEKKIV EEEEEEHVER PEKLISPESE EKWFESRTLD EKVLGHEGDA DMYEWDPNTM TETLVREPPS ...String:
MSRDVSLSPK SGDIRFNGTE PPVKVEVVDE EQSSLNNQLG FSTTLSTSFV LSEDLSESID DLTVTSKDKK KLRPSKVAED IGRKRKDTTN SITNFFHRFT RGDREEKKIV EEEEEEHVER PEKLISPESE EKWFESRTLD EKVLGHEGDA DMYEWDPNTM TETLVREPPS PLEPSSMIFE EKGMLKLLED FRNGELRWLD APQISALGKV KEAHEDVSNI HLQVYEIESA RRKKRKQARS VKENFEFSDS DDSEEEREIE RLFESMNTHM IDMHSALDTV PFYDASQNQR TEKIDNDEEY FSS

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMTrisTris
0.02 %GDNGDN
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146403
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