[English] 日本語
Yorodumi
- PDB-24vc: Structure of lumen-open ABCD4-LMBD1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / peroxisome organization / AP-2 adaptor complex binding / protein transporter activity / clathrin heavy chain binding / protein localization to lysosome / clathrin-coated endocytic vesicle / cobalamin binding / clathrin-dependent endocytosis / clathrin-coated vesicle / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / gastrulation / ATPase-coupled transmembrane transporter activity / 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: Qiwei Liu / Xingfan Li / Yingjie Wu / Kai Zheng / Mi Zhou / Tao Long /
Abstract: Correct trafficking of lysosomal transporters is essential for intracellular homeostasis. While most lysosomal membrane proteins are directed to the lysosome via sorting motifs, the cobalamin ...Correct trafficking of lysosomal transporters is essential for intracellular homeostasis. While most lysosomal membrane proteins are directed to the lysosome via sorting motifs, the cobalamin exporter ABCD4 is distinct, instead relying on LMBD1 as a dedicated chaperone for its trafficking. Dysfunction of either protein causes inherited cobalamin metabolism disorders. Despite its physiological significance, the molecular mechanism underlying this chaperone-dependent trafficking remains unclear. Here, we report the cryo-EM structures of ABCD4 complex with LMBD1 in the lumen-open, substrate-bound and cytosol-open states. LMBD1 contains nine transmembrane-helices (TMs) and a cytosolic domain, both of which engage ABCD4. Cell imaging shows that disruption of these interactions impairs the trafficking of ABCD4 to lysosomes. Structural and biochemical analyses provide insights into cobalamin recognition and reveal conformational states associated with the proposed cobalamin transport cycle. These findings provide molecular insights into cobalamin metabolism and illustrate a chaperone-assisted mechanism that supports proper trafficking of a lysosomal transporter.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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)

+
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