[English] 日本語
Yorodumi
- EMDB-69835: Structure of lumen-open ABCD4-LMBD1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-69835
TitleStructure of lumen-open ABCD4-LMBD1 complex
Map data
Sample
  • Complex: ABCD4-LMBD1 complex
    • Protein or peptide: Lysosomal cobalamin transporter ABCD4
    • Protein or peptide: Lysosomal cobalamin transport escort protein LMBD1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
KeywordsTransporter / MEMBRANE PROTEIN
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
Lysosomal cobalamin transporter ABCD4 / Lysosomal cobalamin transport escort protein LMBD1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLong T / Liu Q
Funding support1 items
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, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_69835.png

Downloads & links

-
Map

FileDownload / File: emd_69835.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127
Minimum - Maximum-1.0947927 - 1.9619639
Average (Standard dev.)0.0009795884 (±0.032093134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_69835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_69835_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ABCD4-LMBD1 complex

EntireName: ABCD4-LMBD1 complex
Components
  • Complex: ABCD4-LMBD1 complex
    • Protein or peptide: Lysosomal cobalamin transporter ABCD4
    • Protein or peptide: Lysosomal cobalamin transport escort protein LMBD1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL

-
Supramolecule #1: ABCD4-LMBD1 complex

SupramoleculeName: ABCD4-LMBD1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Lysosomal cobalamin transporter ABCD4

MacromoleculeName: Lysosomal cobalamin transporter ABCD4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type vitamin B12 transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.693148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVAGPAPGA GARPRLDLQF LQRFLQILKV LFPSWSSQNA LMFLTLLCLT LLEQFVIYQV GLIPSQYYGV LGNKDLEGFK TLTFLAVML IVLNSTLKSF DQFTCNLLYV SWRKDLTEHL HRLYFRGRAY YTLNVLRDDI DNPDQRISQD VERFCRQLSS M ASKLIISP ...String:
MAVAGPAPGA GARPRLDLQF LQRFLQILKV LFPSWSSQNA LMFLTLLCLT LLEQFVIYQV GLIPSQYYGV LGNKDLEGFK TLTFLAVML IVLNSTLKSF DQFTCNLLYV SWRKDLTEHL HRLYFRGRAY YTLNVLRDDI DNPDQRISQD VERFCRQLSS M ASKLIISP FTLVYYTYQC FQSTGWLGPV SIFGYFILGT VVNKTLMGPI VMKLVHQEKL EGDFRFKHMQ IRVNAEPAAF YR AGHVEHM RTDRRLQRLL QTQRELMSKE LWLYIGINTF DYLGSILSYV VIAIPIFSGV YGDLSPTELS TLVSKNAFVC IYL ISCFTQ LIDLSTTLSD VAGYTHRIGQ LRETLLDMSL KSQDCEILGE SKWGLDTPPG WPAAEPADTA FLLERVSISA PSSD KPLIK DLSLKISEGQ SLLITGNTGT GKTSLLRVLG GLWTSTRGSV QMLTDFGPHG VLFLPQKPFF TDGTLREQVI YPLKE VYPD SGSADDERIL RFLELAGLSN LVARTEGLDQ QVDWNWYDVL SPGEMQRLSF ARLFYLQPKY AVLDQATSAL TEEVES ELY RIGQQLGMTF ISVGHRQSLE KFHSLVLKLC GGGRWELMRI KVE

UniProtKB: Lysosomal cobalamin transporter ABCD4

-
Macromolecule #2: Lysosomal cobalamin transport escort protein LMBD1

MacromoleculeName: Lysosomal cobalamin transport escort protein LMBD1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.431395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATSGAASAE LVIGWCIFGL LLLAILAFCW IYVRKYQSRR ESEVVSTITA IFSLAIALIT SALLPVDIFL VSYMKNQNGT FKDWANANV SRQIEDTVLY GYYTLYSVIL FCVFFWIPFV YFYYEEKDDD DTSKCTQIKT ALKYTLGFVV ICALLLLVGA F VPLNVPNN ...String:
MATSGAASAE LVIGWCIFGL LLLAILAFCW IYVRKYQSRR ESEVVSTITA IFSLAIALIT SALLPVDIFL VSYMKNQNGT FKDWANANV SRQIEDTVLY GYYTLYSVIL FCVFFWIPFV YFYYEEKDDD DTSKCTQIKT ALKYTLGFVV ICALLLLVGA F VPLNVPNN KNSTEWEKVK SLFEELGSSH GLAALSFSIS SLTLIGMLAA ITYTAYGMSA LPLNLIKGTR SAAYERLENT ED IEEVEQH IQTIKSKSKD GRPLPARDKR ALKQFEERLR TLKKRERHLE FIENSWWTKF CGALRPLKIV WGIFFILVAL LFV ISLFLS NLDKALHSAG IDSGFIIFGA NLSNPLNMLL PLLQTVFPLD YILITIIIMY FIFTSMAGIR NIGIWFFWVR LYKI RRGRT RPQALLFLCM ILLLIVLHTS YMIYSLAPQY VMYGSQNYLI ETNITSDNHK GNSTLSVPKR CDADAPEDQC TVTRT YLFL HKFWFFSAAY YFGNWAFLGV FLIGLIVSCC KGKKSVIEGV DEDSDISDDE PSVYSA

UniProtKB: Lysosomal cobalamin transport escort protein LMBD1

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: GATAN K3 (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: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jbj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 235141
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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