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- PDB-8xxq: Structural of methylmalonate semialdehyde dehydrogenase ALDH6A1 -

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Basic information

Entry
Database: PDB / ID: 8xxq
TitleStructural of methylmalonate semialdehyde dehydrogenase ALDH6A1
ComponentsMethylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
KeywordsHYDROLASE / dehydrogenase / ALDH6A1
Function / homology
Function and homology information


valine metabolic process / thymine metabolic process / malonate-semialdehyde dehydrogenase (acetylating) activity / methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / thymine catabolic process / valine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / brown fat cell differentiation ...valine metabolic process / thymine metabolic process / malonate-semialdehyde dehydrogenase (acetylating) activity / methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / thymine catabolic process / valine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / brown fat cell differentiation / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Methylmalonate-semialdehyde dehydrogenase / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSu, G. / Xu, Y. / Luan, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902085 China
CitationJournal: Medicine Plus / Year: 2024
Title: Structural and biochemical basis of methylmalonate semialdehyde dehydrogenase ALDH6A1
Authors: Su, G. / Ju, K. / Xu, Y. / Jin, Y. / Chen, L. / Zhang, S. / Luan, X.
History
DepositionJan 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
B: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
C: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
D: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial


Theoretical massNumber of molelcules
Total (without water)216,5854
Polymers216,5854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial / MMSDH / Aldehyde dehydrogenase family 6 member A1 / Malonate-semialdehyde dehydrogenase [acylating]


Mass: 54146.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH6A1, MMSDH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02252, methylmalonate-semialdehyde dehydrogenase (CoA-acylating)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: ALDH6A1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00115480
ELECTRON MICROSCOPYf_angle_d0.40420988
ELECTRON MICROSCOPYf_dihedral_angle_d8.1385732
ELECTRON MICROSCOPYf_chiral_restr0.0412388
ELECTRON MICROSCOPYf_plane_restr0.0022732

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