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Yorodumi- EMDB-25130: Cryo-EM structure of ATP-bound human peroxisomal fatty acid trans... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25130 | ||||||||||||
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Title | Cryo-EM structure of ATP-bound human peroxisomal fatty acid transporter ABCD1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information ABC-type fatty-acyl-CoA transporter activity / peroxisomal membrane transport / very long-chain fatty-acyl-CoA catabolic process / long-chain fatty acid catabolic process / positive regulation of unsaturated fatty acid biosynthetic process / Linoleic acid (LA) metabolism / Defective ABCD1 causes ALD / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / alpha-linolenic acid metabolic process ...ABC-type fatty-acyl-CoA transporter activity / peroxisomal membrane transport / very long-chain fatty-acyl-CoA catabolic process / long-chain fatty acid catabolic process / positive regulation of unsaturated fatty acid biosynthetic process / Linoleic acid (LA) metabolism / Defective ABCD1 causes ALD / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / alpha-linolenic acid metabolic process / alpha-linolenic acid (ALA) metabolism / regulation of fatty acid beta-oxidation / Beta-oxidation of very long chain fatty acids / Class I peroxisomal membrane protein import / very long-chain fatty acid metabolic process / sterol homeostasis / 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 / positive regulation of fatty acid beta-oxidation / regulation of oxidative phosphorylation / linoleic acid metabolic process / 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 / negative regulation of cytokine production involved in inflammatory response / fatty acid homeostasis / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / ADP binding / mitochondrial membrane / peroxisome / protein heterodimerization activity / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | ||||||||||||
Authors | Wang R / Li X | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Res / Year: 2022 Title: Structural basis of acyl-CoA transport across the peroxisomal membrane by human ABCD1. Authors: Rong Wang / Yu Qin / Xiaochun Li / | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25130.map.gz | 72.3 MB | EMDB map data format | |
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Header (meta data) | emd-25130-v30.xml emd-25130.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_25130.png | 13.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25130 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25130 | HTTPS FTP |
-Related structure data
Related structure data | 7shmMC 7shnC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25130.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.844 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ATP-bound human ABCD1 E630Q
Entire | Name: ATP-bound human ABCD1 E630Q |
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Components |
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-Supramolecule #1: ATP-bound human ABCD1 E630Q
Supramolecule | Name: ATP-bound human ABCD1 E630Q / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: ATP-binding cassette sub-family D member 1
Macromolecule | Name: ATP-binding cassette sub-family D member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ec: 7.6.2.4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.036852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKP VLSRPRPWRG NTLKRTAVLL ALAAYGAHKV YPLVRQCLAP ARGLQAPAGE PTQEASGVAA AKAGMNRVFL QRLLWLLRL LFPRVLCRET GLLALHSAAL VSRTFLSVYV ARLDGRLARC IVRKDPRAFG WQLLQWLLIA LPATFVNSAI R YLEGQLAL ...String: MDYKDDDDKP VLSRPRPWRG NTLKRTAVLL ALAAYGAHKV YPLVRQCLAP ARGLQAPAGE PTQEASGVAA AKAGMNRVFL QRLLWLLRL LFPRVLCRET GLLALHSAAL VSRTFLSVYV ARLDGRLARC IVRKDPRAFG WQLLQWLLIA LPATFVNSAI R YLEGQLAL SFRSRLVAHA YRLYFSQQTY YRVSNMDGRL RNPDQSLTED VVAFAASVAH LYSNLTKPLL DVAVTSYTLL RA ARSRGAG TAWPSAIAGL VVFLTANVLR AFSPKFGELV AEEARRKGEL RYMHSRVVAN SEEIAFYGGH EVELALLQRS YQD LASQIN LILLERLWYV MLEQFLMKYV WSASGLLMVA VPIITATGYS ESDAEAVKKA ALEKKEEELV SERTEAFTIA RNLL TAAAD AIERIMSSYK EVTELAGYTA RVHEMFQVFE DVQRCHFKRP RELEDAQAGS GTIGRSGVRV EGPLKIRGQV VDVEQ GIIC ENIPIVTPSG EVVVASLNIR VEEGMHLLIT GPNGCGKSSL FRILGGLWPT YGGVLYKPPP QRMFYIPQRP YMSVGS LRD QVIYPDSVED MQRKGYSEQD LEAILDVVHL HHILQREGGW EAMCDWKDVL SGGEKQRIGM ARMFYHRPKY ALLDQCT SA VSIDVEGKIF QAAKDAGIAL LSITHRPSLW KYHTHLLQFD GEGGWKFEKL DSAARLSLTE EKQRLEQQLA GIPKMQRR L QELCQILGEA VAPAHVPAPS PQGPGGLQGA ST |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247022 |