[English] 日本語
Yorodumi
- PDB-8v3v: ACAD11 D753N with 4-phosphovaleryl-CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v3v
TitleACAD11 D753N with 4-phosphovaleryl-CoA
ComponentsAcyl-Coenzyme A dehydrogenase family, member 11
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenases / Dihedral / mitochondrial
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
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase family member 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang, J. / Bartlett, A. / Rashan, E. / Yuan, P. / Pagliarini, D.
Funding support United States, 3items
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: To Be Published
Title: ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Authors: Bartlett, A. / Rashan, E. / Zhang, J. / Yuan, P. / Pagliarini, D.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl-Coenzyme A dehydrogenase family, member 11
B: Acyl-Coenzyme A dehydrogenase family, member 11
C: Acyl-Coenzyme A dehydrogenase family, member 11
D: Acyl-Coenzyme A dehydrogenase family, member 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,4718
Polymers349,3294
Non-polymers3,1424
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROLEULEUCC54 - 77553 - 774
d_12FADFADFADFADCG801
d_21PROPROLEULEUBB54 - 77553 - 774
d_22FADFADFADFADBF801
d_31PROPROLEULEUAA54 - 77553 - 774
d_32FADFADFADFADAE801
d_41PROPROLEULEUDD54 - 77553 - 774
d_42FADFADFADFADDH801

NCS oper:
IDCodeMatrixVector
1given(-1), (-1), (1)330, 330
2given(-1), (1), (-1)330, -2.84217094304E-14, 330
3given(1), (-1), (-1)330, 330

-
Components

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


Mass: 87332.211 Da / Num. of mol.: 4 / Mutation: D753N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acad11 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4J0I6
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: ACAD11 D753N with FAD and 4-phosphovaleryl-CoA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 50mM HEPES, 50mM NaCl, 2% glycerol, 50uM FAD, 100uM 4-phosphovaleryl-CoA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.06 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 2965

-
Processing

EM software
IDNameVersionCategory
7Coot0.9.8model fitting
19PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1294186
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 297619 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingAccession code: AF-Q80XL6-F1 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001914680
ELECTRON MICROSCOPYf_angle_d0.426420140
ELECTRON MICROSCOPYf_chiral_restr0.03852544
ELECTRON MICROSCOPYf_plane_restr0.00242548
ELECTRON MICROSCOPYf_dihedral_angle_d3.00682288
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints5.87321359596E-13
ens_1d_3CCELECTRON MICROSCOPYNCS constraints2.25479479974E-13
ens_1d_4CCELECTRON MICROSCOPYNCS constraints6.05560634446E-13

+
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