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- EMDB-25131: Cryo-EM structure of oleoyl-CoA-bound human peroxisomal fatty aci... -

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Basic information

Entry
Database: EMDB / ID: EMD-25131
TitleCryo-EM structure of oleoyl-CoA-bound human peroxisomal fatty acid transporter ABCD1
Map data
Sample
  • Complex: oleoyl-CoA-bound human ABCD1 E630Q
    • Protein or peptide: ATP-binding cassette sub-family D member 1
  • Ligand: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)
KeywordsABC transporter / ABCD / acyl-CoA transport / LIPID TRANSPORT
Function / homology
Function and homology information


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 / long-chain fatty acid import into peroxisome ...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 / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / alpha-linolenic acid (ALA) metabolism / regulation of fatty acid beta-oxidation / Beta-oxidation of very long chain fatty acids / sterol homeostasis / Class I peroxisomal membrane protein import / very long-chain fatty acid metabolic process / peroxisome organization / regulation of mitochondrial depolarization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / 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 / fatty acid elongation / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / 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 / 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
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang R / Li X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch Foundation United States
Damon Runyon Cancer Research Foundation United States
CitationJournal: 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
DepositionOct 9, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7shn
  • Surface level: 0.26
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25131.png

Downloads & links

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Map

FileDownload / File: emd_25131.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 272 pix.
= 229.568 Å		0.84 Å/pix.
x 272 pix.
= 229.568 Å		0.84 Å/pix.
x 272 pix.
= 229.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.244 / Movie #1: 0.26
Minimum - Maximum-1.9454465 - 3.0470703
Average (Standard dev.)0.008461008 (±0.07112861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 229.568 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8440.8440.844
M x/y/z272272272
origin x/y/z0.0000.0000.000
length x/y/z229.568229.568229.568
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS272272272
D min/max/mean-1.9453.0470.008

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Supplemental data

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Sample components

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Entire : oleoyl-CoA-bound human ABCD1 E630Q

EntireName: oleoyl-CoA-bound human ABCD1 E630Q
Components
  • Complex: oleoyl-CoA-bound human ABCD1 E630Q
    • Protein or peptide: ATP-binding cassette sub-family D member 1
  • Ligand: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)

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Supramolecule #1: oleoyl-CoA-bound human ABCD1 E630Q

SupramoleculeName: oleoyl-CoA-bound human ABCD1 E630Q / 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 1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.606836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 DS(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

UniProtKB: ATP-binding cassette sub-family D member 1

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Macromolecule #2: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydrox...

MacromoleculeName: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza- ...Name: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)
type: ligand / ID: 2 / Number of copies: 2 / Formula: 3VV
Molecular weightTheoretical: 1.03198 KDa
Chemical component information

ChemComp-3VV:
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 316014
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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