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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
SampleHuman ABCD4
  • ATP-binding cassette sub-family D member 4
  • ligand
Function / homology
Function and homology information


Defective ABCD4 causes methylmalonic aciduria and homocystinuria, cblj type (MAHCJ) / Cobalamin (Cbl, vitamin B12) transport and metabolism / cobalamin metabolic process / peroxisomal membrane / ATPase-coupled transmembrane transporter activity / cellular response to leukemia inhibitory factor / ATP-binding cassette (ABC) transporter complex / peroxisome / lysosomal membrane / transmembrane transport ...Defective ABCD4 causes methylmalonic aciduria and homocystinuria, cblj type (MAHCJ) / Cobalamin (Cbl, vitamin B12) transport and metabolism / cobalamin metabolic process / peroxisomal membrane / ATPase-coupled transmembrane transporter activity / cellular response to leukemia inhibitory factor / ATP-binding cassette (ABC) transporter complex / peroxisome / lysosomal membrane / transmembrane transport / ATPase activity / endoplasmic reticulum membrane / integral component of membrane / ATP binding
AAA+ ATPase domain / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter transmembrane region 2 / ABC transporter / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / ABC transporter-like
ATP-binding cassette sub-family D member 4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu D / Feng Z / Hou WT / Jiang YL / Wang L / Sun LF / Zhou CZ / Chen Y
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910103 China
National Natural Science Foundation of China31621002 China
Chinese Academy of SciencesXDB08020304 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 /
Validation ReportPDB-ID: 6jbj

SummaryFull reportAbout validation report
History
DepositionJan 25, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateSep 11, 2019-
Current statusSep 11, 2019Processing 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
  • Download
  • 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

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
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 / Number of components: 3

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Component #1: protein, Human ABCD4

ProteinName: Human ABCD4 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, ATP-binding cassette sub-family D member 4

ProteinName: ATP-binding cassette sub-family D member 4 / Details: ATPAdenosine triphosphate / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 73.123719 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 276557
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Overall bvalue: 199
Output model

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