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- PDB-8z9x: Cryo-EM structure of Phytanoyl-CoA-bound human very long-chain fa... -

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Basic information

Entry
Database: PDB / ID: 8z9x
TitleCryo-EM structure of Phytanoyl-CoA-bound human very long-chain fatty acid ABC transporter ABCD3
ComponentsATP-binding cassette sub-family D member 3
KeywordsTRANSPORT PROTEIN / very long-chain fatty / Peroxisome / 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 / Class I peroxisomal membrane protein import / very long-chain fatty acid metabolic process / 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 / Class I peroxisomal membrane protein import / very long-chain fatty acid metabolic process / 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 / bile acid and bile salt transport / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / RHOC GTPase cycle / peroxisomal matrix / ATPase-coupled transmembrane transporter activity / RHOA GTPase cycle / ABC-type transporter activity / response to organic cyclic compound / fatty acid biosynthetic process / peroxisome / response to xenobiotic stimulus / intracellular membrane-bounded organelle / 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 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLi, Y. / Chen, Y.X. / Zhou, C.Z. / Hou, W.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071206 China
CitationJournal: To Be Published
Title: Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation
Authors: Yang, L. / Wen, T.H.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ATP-binding cassette sub-family D member 3
A: ATP-binding cassette sub-family D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,4824
Polymers153,3582
Non-polymers2,1242
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 76679.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCD3, PMP70, PXMP1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P28288, 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-A1L1A / phytanoyl-CoA / S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethyl] (3S,7R,11R)-3,7,11,15-tetramethylhexadecanethioate / Phytanoyl-coenzyme A


Mass: 1062.049 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H74N7O17P3S
Has ligand of interestN

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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: Phytanoyl-CoA-bound human peroxisomal ABCD3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 140 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96695 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049404
ELECTRON MICROSCOPYf_angle_d0.56112682
ELECTRON MICROSCOPYf_dihedral_angle_d4.8911272
ELECTRON MICROSCOPYf_chiral_restr0.0411394
ELECTRON MICROSCOPYf_plane_restr0.0031600

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