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Basic information

Entry
Database: EMDB / ID: EMD-69837
TitleStructure of cytosol-open ABCD4-LMBD1
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'-DIPHOSPHATE
KeywordsTransporter / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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: Liu Q / Li X / Wu Y / Zheng K / Zhou M / Long T
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_69837.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.738 Å
Density
Contour LevelBy AUTHOR: 0.0623
Minimum - Maximum-0.31993645 - 0.59477234
Average (Standard dev.)0.0017131611 (±0.013612529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 250.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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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'-DIPHOSPHATE

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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)

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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: 68.694141 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 AVLDEATSAL 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'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 0.8 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 347750
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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