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- PDB-24vc: Structure of lumen-open ABCD4-LMBD1 complex -

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Basic information

Entry
Database: PDB / ID: 24vc
TitleStructure of lumen-open ABCD4-LMBD1 complex
Components
  • Lysosomal cobalamin transport escort protein LMBD1
  • Lysosomal cobalamin transporter ABCD4
KeywordsMEMBRANE PROTEIN / Transporter
Function / homology
Function and homology information


Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / insulin receptor internalization / ABC-type vitamin B12 transporter activity / Transport of RCbl within the body / Uptake of dietary cobalamins into enterocytes / cobalamin metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport ...Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / insulin receptor internalization / ABC-type vitamin B12 transporter activity / Transport of RCbl within the body / Uptake of dietary cobalamins into enterocytes / cobalamin metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport / AP-2 adaptor complex binding / peroxisome organization / clathrin heavy chain binding / protein transporter activity / clathrin-coated endocytic vesicle / protein localization to lysosome / cobalamin binding / clathrin-dependent endocytosis / clathrin-coated vesicle / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / gastrulation / ATP-binding cassette (ABC) transporter complex / insulin receptor binding / transmembrane transport / peroxisome / lysosomal membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
LMBR1-like membrane protein / : / LMBR1-like membrane protein / ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. ...LMBR1-like membrane protein / : / LMBR1-like membrane protein / ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CHOLESTEROL / Lysosomal cobalamin transporter ABCD4 / Lysosomal cobalamin transport escort protein LMBD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLong, T. / Liu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for LMBD1-dependent trafficking and cobalamin export of ABCD4.
Authors: Liu, Q. / Li, X. / Wu, Y. / Zheng, K. / Zhou, M. / Long, T.
History
DepositionMar 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysosomal cobalamin transporter ABCD4
B: Lysosomal cobalamin transporter ABCD4
C: Lysosomal cobalamin transport escort protein LMBD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2678
Polymers198,8183
Non-polymers1,4505
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lysosomal cobalamin transporter ABCD4 / ATP-binding cassette sub-family D member 4 / PMP70-related protein / P70R / Peroxisomal membrane ...ATP-binding cassette sub-family D member 4 / PMP70-related protein / P70R / Peroxisomal membrane protein 1-like / PXMP1-L / Peroxisomal membrane protein 69 / PMP69


Mass: 68693.148 Da / Num. of mol.: 2 / Mutation: E549Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCD4, PXMP1L / Production host: Homo sapiens (human)
References: UniProt: O14678, ABC-type vitamin B12 transporter
#2: Protein Lysosomal cobalamin transport escort protein LMBD1 / LMBD1 / HDAg-L-interacting protein NESI / LMBR1 domain-containing protein 1 / Nuclear export signal- ...LMBD1 / HDAg-L-interacting protein NESI / LMBR1 domain-containing protein 1 / Nuclear export signal-interacting protein


Mass: 61431.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMBRD1, C6orf209, NESI, BM-021, CD001, MSTP044 / Production host: Homo sapiens (human) / References: UniProt: Q9NUN5
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
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: ABCD4-LMBD1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235141 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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