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- PDB-9w63: Cryo-EM structure of C20:5-CoA bound state human ABCD3 in inward-... -

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Basic information

Entry
Database: PDB / ID: 9w63
TitleCryo-EM structure of C20:5-CoA bound state human ABCD3 in inward-facing conformation
ComponentsIsoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein
KeywordsTRANSPORT PROTEIN / ABC transporter
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
Chem-3IX / CHOLESTEROL / ATP-binding cassette sub-family D member 3 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsAiba, S. / Okamoto, H.H. / Kusakizako, T. / Nureki, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H06294 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15754 Japan
Japan Society for the Promotion of Science (JSPS)JP25KJ1114 Japan
CitationJournal: To Be Published
Title: Structural Insights into the Broad Substrate Recognition Mechanism of Human ABCD3
Authors: Aiba, S. / Okamoto, H.H. / Tomita, A. / Sano, F. / Kusakizako, T. / Nureki, O.
History
DepositionAug 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Isoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5157
Polymers104,5281
Non-polymers2,9876
Water00
1
A: Isoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein
hetero molecules

A: Isoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,03014
Polymers209,0552
Non-polymers5,97512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate / Matrix: (-1), (-1), (1) / Vector: 332.00012, 332.00012)

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Components

#1: Protein Isoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein / 70 kDa peroxisomal membrane protein / PMP70


Mass: 104527.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCD3, PMP70, PXMP1, GFP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28288, UniProt: P42212, Hydrolases; Acting on ester bonds; Thioester hydrolases, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#2: Chemical ChemComp-3IX / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate / Arachidonyl-CoA


Mass: 1053.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H66N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C20:5-CoA bound ABCD3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
2150 mMSodium chlorideNaCl1
30.3 g/LGlyco-diosgeninGDN1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119378 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.010296319449850.0116864594
ELECTRON MICROSCOPYs_angle_nonh_d1.8860434567551.63018949

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