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Yorodumi- PDB-7vx8: Cryo-EM structure of ATP-bound human very long-chain fatty acid A... -
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-Basic information
Entry | Database: PDB / ID: 7vx8 | ||||||
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Title | Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD1 | ||||||
Components | Peroxisomal Membrane Protein related,ATP-binding cassette sub-family D member 1 | ||||||
Keywords | TRANSPORT PROTEIN / very long-chain fatty / Peroxisome / ABC transporter | ||||||
Function / homology | Function and homology information ABC transporters in lipid homeostasis / Linoleic acid (LA) metabolism / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / Class I peroxisomal membrane protein import / ABC-type fatty-acyl-CoA transporter activity / peroxisomal membrane transport / very long-chain fatty-acyl-CoA catabolic process / very long-chain fatty acyl-CoA hydrolase activity / positive regulation of unsaturated fatty acid biosynthetic process ...ABC transporters in lipid homeostasis / Linoleic acid (LA) metabolism / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / Class I peroxisomal membrane protein import / ABC-type fatty-acyl-CoA transporter activity / peroxisomal membrane transport / very long-chain fatty-acyl-CoA catabolic process / very long-chain fatty acyl-CoA hydrolase activity / positive regulation of unsaturated fatty acid biosynthetic process / Linoleic acid (LA) metabolism / Defective ABCD1 causes ALD / alpha-linolenic acid metabolic process / long-chain fatty acid catabolic process / alpha-linolenic acid (ALA) metabolism / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / Beta-oxidation of very long chain fatty acids / regulation of fatty acid beta-oxidation / very long-chain fatty acid metabolic process / sterol homeostasis / Class I peroxisomal membrane protein import / peroxisome organization / regulation of mitochondrial depolarization / ABC transporters in lipid homeostasis / fatty acyl-CoA hydrolase activity / myelin maintenance / regulation of cellular response to oxidative stress / Hydrolases; Acting on ester bonds; Thioester hydrolases / linoleic acid metabolic process / positive regulation of fatty acid beta-oxidation / regulation of oxidative phosphorylation / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / fatty acid elongation / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / negative regulation of cytokine production involved in inflammatory response / fatty acid homeostasis / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / mitochondrial membrane / ADP binding / peroxisome / protein heterodimerization activity / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Chen, Z.P. / Xu, D. / Wang, L. / Mao, Y.X. / Yang, L. / Cheng, M.T. / Hou, W.T. / Chen, Y.X. / Zhou, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of substrate recognition and translocation by human very long-chain fatty acid transporter ABCD1. Authors: Zhi-Peng Chen / Da Xu / Liang Wang / Yao-Xu Mao / Yang Li / Meng-Ting Cheng / Cong-Zhao Zhou / Wen-Tao Hou / Yuxing Chen / Abstract: Human ABC transporter ABCD1 transports very long-chain fatty acids from cytosol to peroxisome for β-oxidation, dysfunction of which usually causes the X-linked adrenoleukodystrophy (X-ALD). Here, we ...Human ABC transporter ABCD1 transports very long-chain fatty acids from cytosol to peroxisome for β-oxidation, dysfunction of which usually causes the X-linked adrenoleukodystrophy (X-ALD). Here, we report three cryogenic electron microscopy structures of ABCD1: the apo-form, substrate- and ATP-bound forms. Distinct from what was seen in the previously reported ABC transporters, the two symmetric molecules of behenoyl coenzyme A (C22:0-CoA) cooperatively bind to the transmembrane domains (TMDs). For each C22:0-CoA, the hydrophilic 3'-phospho-ADP moiety of CoA portion inserts into one TMD, with the succeeding pantothenate and cysteamine moiety crossing the inter-domain cavity, whereas the hydrophobic fatty acyl chain extends to the opposite TMD. Structural analysis combined with biochemical assays illustrates snapshots of ABCD1-mediated substrate transport cycle. It advances our understanding on the selective oxidation of fatty acids and molecular pathology of X-ALD. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vx8.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vx8.ent.gz | 167.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vx8_validation.pdf.gz | 992 KB | Display | wwPDB validaton report |
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Full document | 7vx8_full_validation.pdf.gz | 1005.3 KB | Display | |
Data in XML | 7vx8_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 7vx8_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/7vx8 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/7vx8 | HTTPS FTP |
-Related structure data
Related structure data | 32171MC 7vwcC 7vzbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 87930.008 Da / Num. of mol.: 2 / Mutation: E630Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata), (gene. exp.) Homo sapiens (human) Gene: pmp-4, CELE_T02D1.5, T02D1.5, ABCD1, ALD / Plasmid: pCAG / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) References: UniProt: O45730, UniProt: P33897, Hydrolases; Acting on ester bonds; Thioester hydrolases, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ATP-bound human peroxisomal ABCD1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 175.6 kDa/nm / Experimental value: NO | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pCAG | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 528247 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.38 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.00070966635215 Å |