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- EMDB-39871: Cryo-EM structure of Phytanoyl-CoA-bound human very long-chain fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-39871
TitleCryo-EM structure of Phytanoyl-CoA-bound human very long-chain fatty acid ABC transporter ABCD3
Map data
Sample
  • Complex: Phytanoyl-CoA-bound human peroxisomal ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3
  • Ligand: phytanoyl-CoA
Keywordsvery long-chain fatty / Peroxisome / ABC transporter / TRANSPORT PROTEIN
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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLi Y / Chen YX / Zhou CZ / Hou WT
Funding support China, 1 items
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 TH
History
DepositionApr 23, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39871.png

Downloads & links

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Map

FileDownload / File: emd_39871.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.371
Minimum - Maximum-1.5638444 - 2.5394604
Average (Standard dev.)-0.00027920963 (±0.05299105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39871_additional_1.map
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Half map: #2

Fileemd_39871_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_39871_half_map_2.map
Projections & Slices
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Sample components

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Entire : Phytanoyl-CoA-bound human peroxisomal ABCD3

EntireName: Phytanoyl-CoA-bound human peroxisomal ABCD3
Components
  • Complex: Phytanoyl-CoA-bound human peroxisomal ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3
  • Ligand: phytanoyl-CoA

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Supramolecule #1: Phytanoyl-CoA-bound human peroxisomal ABCD3

SupramoleculeName: Phytanoyl-CoA-bound human peroxisomal ABCD3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 kDa/nm

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Macromolecule #1: ATP-binding cassette sub-family D member 3

MacromoleculeName: ATP-binding cassette sub-family D member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Thioester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.67918 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKA VFSKLQLLGQ AIPPKQYAPG VVGMLAVFAL IKLYKQDIRG TKHLVAKTKE GKKERAVVDK VFFSRLIQIL KIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK DFKRYLLNFI AAMPLISLVN NFLKYGLNEL K LCFRVRLT ...String:
MDYKDDDDKA VFSKLQLLGQ AIPPKQYAPG VVGMLAVFAL IKLYKQDIRG TKHLVAKTKE GKKERAVVDK VFFSRLIQIL KIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK DFKRYLLNFI AAMPLISLVN NFLKYGLNEL K LCFRVRLT KYLYEEYLQA FTYYKMGNLD NRIANPDQLL TQDVEKFCNS VVDLYSNLSK PFLDIVLYIF KLTSAIGAQG PA SMMAYLV VSGLFLTRLR RPIGKMTITE QKYEGEYRYV NSRLITNSEE IAFYNGNKRE KQTVHSVFRK LVEHLHNFIL FRF SMGFID SIIAKYLATV VGYLVVSRPF LDLSHPRHLK STHSELLEDY YQSGRMLLRM SQALGRIVLA GREMTRLAGF TARI TELMQ VLKDLNHGKY ERTMVSQQEK GIEGVQVIPL IPGAGEIIIA DNIIKFDHVP LATPNGDVLI RDLNFEVRSG ANVLI CGPN GCGKSSLFRV LGELWPLFGG RLTKPERGKL FYVPQRPYMT LGTLRDQVIY PDGREDQKRK GISDLVLKEY LDNVQL GHI LEREGGWDSV QDWMDVLSGG EKQRMAMARL FYHKPQFAIL DECTSAVSVD VEGYIYSHCR KVGITLFTVS HRKSLWK HH EYYLHMDGRG NYEFKQITED TVEFGS

UniProtKB: ATP-binding cassette sub-family D member 3

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Macromolecule #2: phytanoyl-CoA

MacromoleculeName: phytanoyl-CoA / type: ligand / ID: 2 / Number of copies: 2 / Formula: A1L1A
Molecular weightTheoretical: 1.062049 KDa

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96695
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5

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