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- EMDB-9791: Cryo-EM structure of human lysosomal cobalamin exporter ABCD4 -

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Basic information

Entry
Database: EMDB / ID: EMD-9791
TitleCryo-EM structure of human lysosomal cobalamin exporter ABCD4
Map data
Sample
  • Complex: Human ABCD4
    • Protein or peptide: ATP-binding cassette sub-family D member 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsHuman ABCD4 / Lysosomal cobalamin exporter / ATP-bound / lysosome-open conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport / peroxisome organization ...Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport / peroxisome organization / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cellular response to leukemia inhibitory factor / transmembrane transport / peroxisome / lysosomal membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / identical protein binding / membrane
Similarity search - Function
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. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu D / Feng Z
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910103 China
Chinese Academy of SciencesXDB08020304 China
National Natural Science Foundation of China31621002 China
CitationJournal: Cell Res / Year: 2019
Title: Cryo-EM structure of human lysosomal cobalamin exporter ABCD4.
Authors: Da Xu / Zhang Feng / Wen-Tao Hou / Yong-Liang Jiang / Liang Wang / Linfeng Sun / Cong-Zhao Zhou / Yuxing Chen /
History
DepositionJan 25, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jbj
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9791.png

Downloads & links

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Map

FileDownload / File: emd_9791.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.04
Minimum - Maximum-0.094036005 - 0.16849421
Average (Standard dev.)0.00010282971 (±0.0064872955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0940.1680.000

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Supplemental data

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Sample components

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Entire : Human ABCD4

EntireName: Human ABCD4
Components
  • Complex: Human ABCD4
    • Protein or peptide: ATP-binding cassette sub-family D member 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Human ABCD4

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

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Macromolecule #1: ATP-binding cassette sub-family D member 4

MacromoleculeName: ATP-binding cassette sub-family D member 4 / type: protein_or_peptide / ID: 1 / Details: ATP / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.123719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTAVAGPAP GAGARPRLDL QFLQRFLQIL KVLFPSWSSQ NALMFLTLL CLTLLEQFVI YQVGLIPSQY YGVLGNKDLE GFKTLTFLAV MLIVLNSTLK SFDQFTCNLL YVSWRKDLTE H LHRLYFRG ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTAVAGPAP GAGARPRLDL QFLQRFLQIL KVLFPSWSSQ NALMFLTLL CLTLLEQFVI YQVGLIPSQY YGVLGNKDLE GFKTLTFLAV MLIVLNSTLK SFDQFTCNLL YVSWRKDLTE H LHRLYFRG RAYYTLNVLR DDIDNPDQRI SQDVERFCRQ LSSMASKLII SPFTLVYYTY QCFQSTGWLG PVSIFGYFIL GT VVNKTLM GPIVMKLVHQ EKLEGDFRFK HMQIRVNAEP AAFYRAGHVE HMRTDRRLQR LLQTQRELMS KELWLYIGIN TFD YLGSIL SYVVIAIPIF SGVYGDLSPA ELSTLVSKNA FVCIYLISCF TQLIDLSTTL SDVAGYTHRI GQLRETLLDM SLKS QDCEI LGESEWGLDT PPGWPAAEPA DTAFLLERVS ISAPSSDKPL IKDLSLKISE GQSLLITGNT GTGKTSLLRV LGGLW TSTR GSVQMLTDFG PHGVLFLPQK PFFTDGTLRE QVIYPLKEVY PDSGSADDER ILRFLELAGL SNLVARTEGL DQQVDW NWY DVLSPGEMQR LSFARLFYLQ PKYAVLDQAT SALTEEVESE LYRIGQQLGM TFISVGHRQS LEKFHSLVLK LCGGGRW EL MRIKVE

UniProtKB: Lysosomal cobalamin transporter ABCD4

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (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: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 276557
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 199
Output model

PDB-6jbj:
Cryo-EM structure of human lysosomal cobalamin exporter ABCD4

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