[English] 日本語
Yorodumi
- EMDB-16515: Cryo-EM structure of the ACADVL dimer from Mus musculus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16515
TitleCryo-EM structure of the ACADVL dimer from Mus musculus.
Map dataglobally sharpened map (locally refined).
Sample
  • Complex: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
    • Protein or peptide: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
KeywordsNADH ubiquinone oxidoreductase / Complex I / OXIDOREDUCTASE
Function / homology
Function and homology information


Beta oxidation of palmitoyl-CoA to myristoyl-CoA / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / fatty acid catabolic process / negative regulation of fatty acid biosynthetic process ...Beta oxidation of palmitoyl-CoA to myristoyl-CoA / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / fatty acid catabolic process / negative regulation of fatty acid biosynthetic process / regulation of cholesterol metabolic process / temperature homeostasis / fatty acid beta-oxidation / mitochondrial nucleoid / epithelial cell differentiation / response to cold / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / nucleolus / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYin Z / Bridges HR / Agip ANA / Hirst J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105663141 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: EMBO J / Year: 2024
Title: Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 mouse.
Authors: Zhan Yin / Ahmed-Noor A Agip / Hannah R Bridges / Judy Hirst /
Abstract: Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh ...Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, the ndufs4 mouse, to define the structural, biochemical, and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of the complex I from ndufs4 mouse hearts revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12, which replaces its paralogue NDUFAF2 in mature complex I, is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free enzyme. We propose that NDUFAF2 recruits the NADH-dehydrogenase module during assembly of the complex. Taken together, the findings provide new molecular-level understanding of the ndufs4 mouse model and complex I-linked mitochondrial disease.
History
DepositionJan 24, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16515.png

Downloads & links

-
Map

FileDownload / File: emd_16515.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationglobally sharpened map (locally refined).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 450 pix.
= 608.4 Å		1.35 Å/pix.
x 450 pix.
= 608.4 Å		1.35 Å/pix.
x 450 pix.
= 608.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.352 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-2.3057506 - 4.9198847
Average (Standard dev.)0.0009581706 (±0.25442776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 608.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16515_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_16515_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_16515_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Very long-chain specific acyl-CoA dehydrogenase, mitochondrial

EntireName: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Components
  • Complex: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
    • Protein or peptide: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide

-
Supramolecule #1: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial

SupramoleculeName: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial

MacromoleculeName: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: very-long-chain acyl-CoA dehydrogenase
Source (natural)Organism: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 70.959375 KDa
SequenceString: MQSARMTPSV GRQLLRLGAR SSRSTTVLQG QPRPISAQRL YAREATQAVL DKPETLSSDA STREKPARAE SKSFAVGMFK GQLTIDQVF PYPSVLSEEQ AQFLKELVGP VARFFEEVND PAKNDALEKV EDDTLQGLKE LGAFGLQVPS ELGGLGLSNT Q YARLAEIV ...String:
MQSARMTPSV GRQLLRLGAR SSRSTTVLQG QPRPISAQRL YAREATQAVL DKPETLSSDA STREKPARAE SKSFAVGMFK GQLTIDQVF PYPSVLSEEQ AQFLKELVGP VARFFEEVND PAKNDALEKV EDDTLQGLKE LGAFGLQVPS ELGGLGLSNT Q YARLAEIV GMHDLGVSVT LGAHQSIGFK GILLYGTKAQ REKYLPRVAS GQALAAFCLT EPSSGSDVAS IRSSAIPSPC GK YYTLNGS KIWISNGGLA DIFTVFAKTP IKDAATGAVK EKITAFVVER SFGGVTHGLP EKKMGIKASN TSEVYFDGVK VPS ENVLGE VGDGFKVAVN ILNNGRFGMA ATLAGTMKSL IAKAVDHATN RTQFGDKIHN FGVIQEKLAR MAILQYVTES MAYM LSANM DQGFKDFQIE AAISKIFCSE AAWKVADECI QIMGGMGFMK EPGVERVLRD IRIFRIFEGA NDILRLFVAL QGCMD KGKE LTGLGNALKN PFGNVGLLMG EAGKQLRRRT GIGSGLSLSG IVHPELSRSG ELAVQALDQF ATVVEAKLVK HKKGIV NEQ FLLQRLADGA IDLYAMVVVL SRASRSLSEG YPTAQHEKML CDSWCIEAAT RIRENMASLQ SSPQHQELFR NFRSISK AM VENGGLVTGN PLGI

UniProtKB: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

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

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.82 mg/mL
BufferpH: 7.14
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3tris
150.0 mMNaClSodium chloridesodium chloride
0.05 %C24H46O11DDM
2.5 mMC16H19N2NaO14S2BS3

Details: pH was corrected at room temperature ~22 C
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Details: ACADVL is associated with complex I and the startup model used was EMD-11377.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8793
FSC plot (resolution estimation)

+
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