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- EMDB-65678: Cryo-EM structure of ATP bound state human ABCD3 in outward-facin... -

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Basic information

Entry
Database: EMDB / ID: EMD-65678
TitleCryo-EM structure of ATP bound state human ABCD3 in outward-facing conformation
Map data
Sample
  • Complex: ATP bound ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3,Green fluorescent protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
KeywordsABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases ...phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / bile acid and bile salt transport / fatty acid beta-oxidation / RHOC GTPase cycle / peroxisomal matrix / ATPase-coupled transmembrane transporter activity / RHOA GTPase cycle / ABC-type transporter activity / bioluminescence / generation of precursor metabolites and energy / fatty acid biosynthetic process / peroxisome / response to xenobiotic stimulus / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytosol
Similarity search - Function
Peroxysomal long chain fatty acyl transporter / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Peroxysomal long chain fatty acyl transporter / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
ATP-binding cassette sub-family D member 3 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAiba S / Okamoto HH / Tomita A / Kusakizako T / Nureki O
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H06294 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15754 Japan
CitationJournal: To Be Published
Title: Structural Insights into the Broad Substrate Recognition Mechanism of Human ABCD3
Authors: Aiba S / Okamoto HH / Tomita A / Sano F / Kusakizako T / Nureki O
History
DepositionAug 3, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65678.png

Downloads & links

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Map

FileDownload / File: emd_65678.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 96 pix.
= 145.195 Å		1.51 Å/pix.
x 74 pix.
= 111.921 Å		1.51 Å/pix.
x 82 pix.
= 124.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.51244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6
Minimum - Maximum-4.601304 - 7.0095434
Average (Standard dev.)-0.026347267 (±0.5349931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin515150
Dimensions748296
Spacing827496
CellA: 124.02046 Å / B: 111.9209 Å / C: 145.19469 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65678_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65678_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65678_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP bound ABCD3

EntireName: ATP bound ABCD3
Components
  • Complex: ATP bound ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3,Green fluorescent protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: ATP bound ABCD3

SupramoleculeName: ATP bound ABCD3 / 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 3,Green fluorescent protein

MacromoleculeName: ATP-binding cassette sub-family D member 3,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Thioester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.526641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ ...String:
MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ AFTYYKMGNL DNRIANPDQL LTQDVEKFCN SVVDLYSNLS KPFLDIVLYI FKLTSAIGAQ GPASMMAYLV VS GLFLTRL RRPIGKMTIT EQKYEGEYRY VNSRLITNSE EIAFYNGNKR EKQTVHSVFR KLVEHLHNFI LFRFSMGFID SII AKYLAT VVGYLVVSRP FLDLSHPRHL KSTHSELLED YYQSGRMLLR MSQALGRIVL AGREMTRLAG FTARITELMQ VLKD LNHGK YERTMVSQQE KGIEGVQVIP LIPGAGEIII ADNIIKFDHV PLATPNGDVL IRDLNFEVRS GANVLICGPN GCGKS SLFR VLGELWPLFG GRLTKPERGK LFYVPQRPYM TLGTLRDQVI YPDGREDQKR KGISDLVLKE YLDNVQLGHI LEREGG WDS VQDWMDVLSG GEKQRMAMAR LFYHKPQFAI LDQCTSAVSV DVEGYIYSHC RKVGITLFTV SHRKSLWKHH EYYLHMD GR GNYEFKQITE DTVEFGSLEV LFQGPAVSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGK L PVPWPTLVTT LTYGVQCFSR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKE DGNILGHKLE YNYNSHNVYI MADKQKNGIK VNFKIRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSKLSKDPN EKRDHMVLL EFVTAAGITL GMDELYKHHH HHHHH

UniProtKB: ATP-binding cassette sub-family D member 3, Green fluorescent protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 4 / 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: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClSodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 20043
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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