[English] 日本語
Yorodumi
- EMDB-42954: ACAD11 D220A with 4-hydroxyvaleryl-CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42954
TitleACAD11 D220A with 4-hydroxyvaleryl-CoA
Map data
Sample
  • Complex: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA
    • Protein or peptide: Acyl-Coenzyme A dehydrogenase family, member 11
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Keywordsacyl-CoA dehydrogenases / Dihedral / mitochondrial / OXIDOREDUCTASE
Function / homology
Function and homology information


very-long-chain fatty acyl-CoA dehydrogenase activity / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / mitochondrial membrane / peroxisome / flavin adenine dinucleotide binding / nucleus
Similarity search - Function
Acyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Acyl-CoA dehydrogenase family member 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang J / Bartlett A / Rashan E / Yuan P / Pagliarini D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131795 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK098672 United States
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism.
Authors: Edrees H Rashan / Abigail K Bartlett / Daven B Khana / Jingying Zhang / Raghav Jain / Gina Wade / Luciano A Abriata / Andrew J Smith / Zakery N Baker / Taylor Cook / Alana Caldwell / Autumn ...Authors: Edrees H Rashan / Abigail K Bartlett / Daven B Khana / Jingying Zhang / Raghav Jain / Gina Wade / Luciano A Abriata / Andrew J Smith / Zakery N Baker / Taylor Cook / Alana Caldwell / Autumn R Chevalier / Patrick Forny / Brian F Pfleger / Matteo Dal Peraro / Peng Yuan / Daniel Amador-Noguez / Judith A Simcox / David J Pagliarini /
Abstract: Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation ...Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation machinery before being modified. Here we reveal that two atypical acyl-CoA dehydrogenases, ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains that phosphorylate the 4-hydroxy position as a requisite step in converting 4-hydroxyacyl-CoAs into conventional 2-enoyl-CoAs. Through cryo-electron microscopy and molecular modeling, we identified an atypical dehydrogenase binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma and females are susceptible to body weight and fat gain, concurrent with decreased adipocyte differentiation and adipokine expression. Collectively, we present that ACAD10 and ACAD11 are the primary gatekeepers of mammalian 4-HA catabolism.
History
DepositionNov 28, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42954.png

Downloads & links

-
Map

FileDownload / File: emd_42954.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6
Minimum - Maximum-7.742005 - 12.913852
Average (Standard dev.)-0.00033987008 (±0.23128964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half A

Fileemd_42954_half_map_1.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_42954_half_map_2.map
Annotationhalf_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA

EntireName: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA
Components
  • Complex: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA
    • Protein or peptide: Acyl-Coenzyme A dehydrogenase family, member 11
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

-
Supramolecule #1: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA

SupramoleculeName: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Acyl-Coenzyme A dehydrogenase family, member 11

MacromoleculeName: Acyl-Coenzyme A dehydrogenase family, member 11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 87.289188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ETDVTSDTVE VLPQHKFDLR SLEAYLNQHL PGFGSDSRAV LTVTQYRSGQ SNPTFFLQKG SQAYVLRKKP PGSLLPKAHK IDREFKIQK ALFSIGFPVA KPLLYCRDAS VIGTEFYVME HVQGRIFRDF SIPGVSSAER AAIYVSVAET LAWLHSLDIR S LKLDKYGT ...String:
ETDVTSDTVE VLPQHKFDLR SLEAYLNQHL PGFGSDSRAV LTVTQYRSGQ SNPTFFLQKG SQAYVLRKKP PGSLLPKAHK IDREFKIQK ALFSIGFPVA KPLLYCRDAS VIGTEFYVME HVQGRIFRDF SIPGVSSAER AAIYVSVAET LAWLHSLDIR S LKLDKYGT GVGYCKRQVS TWTKQYQASA HQSIPAMDQL STWLMKNLPD SDSEECLVHG AFKLDNIVFH PKECRVIAVL DW ELSTFGH PLTDLAHLSL FYYWPRTLPM INRGSHIPEN TGIPLMEELI SIYCHRRGID PNLPNWNFFM ALSFFKLAGI SQG VYRRYL MGNNSSEDSF LTANTVQPLA ETGLQLSKRT LRTTPPQADA KSQLFAQSRR GQEVLTRVKQ FMKQHVFPAE KEVA EYYAQ SGNSAEKWGH PLVIEKLKEI AKAEGLWNLF LPAVSGLSQV DYALIAEETG KCFFAPDVFN CQAPDTGNME VLHLY GSEQ QKKQWLEPLL RGDITSVFCM TEPNVSSSDA TNIECTIQRD GGGYIVNGKK WWSSGAGNPK CKIAIVLGRT ESPSAS RHR QHSMILVPMD TPGVELIRPL SVFGYMDNMH GGHWEVHFNH VRVPASNLIL GEGRGFEISQ GRLGPGRIHH CMRTVGL AE RILQIMCDRA VQREAFKKKL YEHEVVAHWI AKSRIAIEEI RLLTLKAAHS IDTLGSASAR KEIAMIKVAA PKAVCKIA D WAIQVHGGAG VSQDYPLANM YAIIRTLRLA DGPDEVHLSA IAKMELQDQA RRLTARM

UniProtKB: Acyl-CoA dehydrogenase family member 11

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Details: 50mM HEPES, 50mM NaCl, 2% glycerol, 50uM FAD, 100uM 4-hydroxyvaleryl-CoA
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 2789 / Average electron dose: 54.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 722751
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2wbi

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242249
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2wbi


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8v3u:
ACAD11 D220A with 4-hydroxyvaleryl-CoA

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more