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- EMDB-69836: Structure of substrate-bound ABCD4-LMBD1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-69836
TitleStructure of substrate-bound ABCD4-LMBD1 complex
Map data
Sample
  • Complex: ABCD4-LMBD1
    • Protein or peptide: Lysosomal cobalamin transporter ABCD4
    • Protein or peptide: Lysosomal cobalamin transport escort protein LMBD1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: COBALAMIN
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
KeywordsTransporter / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 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

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Structure visualization

Supplemental images

emd_69836.png

Downloads & links

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Map

FileDownload / File: emd_69836.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-1.041455 - 2.1191165
Average (Standard dev.)0.001622999 (±0.030622087)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_69836_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69836_half_map_2.map
Projections & Slices
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Sample components

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Entire : ABCD4-LMBD1

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

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Supramolecule #1: ABCD4-LMBD1

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

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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

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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

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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

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Macromolecule #4: COBALAMIN

MacromoleculeName: COBALAMIN / type: ligand / ID: 4 / Number of copies: 1 / Formula: B12
Molecular weightTheoretical: 1.330356 KDa
Chemical component information

ChemComp-B12:
COBALAMIN

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

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

6jbj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 185771
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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