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- EMDB-38758: Structural of methylmalonate semialdehyde dehydrogenase ALDH6A1 -

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Basic information

Entry
Database: EMDB / ID: EMD-38758
TitleStructural of methylmalonate semialdehyde dehydrogenase ALDH6A1
Map data
Sample
  • Complex: ALDH6A1
    • Protein or peptide: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
Keywordsdehydrogenase / ALDH6A1 / HYDROLASE
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 / L-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 / L-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSu G / Xu Y / Luan X
Funding support China, 1 items
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, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38758.png

Downloads & links

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Map

FileDownload / File: emd_38758.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.27035826 - 0.7749448
Average (Standard dev.)0.001176223 (±0.03699017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38758_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38758_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ALDH6A1

EntireName: ALDH6A1
Components
  • Complex: ALDH6A1
    • Protein or peptide: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial

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Supramolecule #1: ALDH6A1

SupramoleculeName: ALDH6A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [...

MacromoleculeName: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.146129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SSVPTVKLFI GGKFVESKSD KWIDIHNPAT NEVIGRVPQA TKAEMDAAIA SCKRAFPAWA DTSVLSRQQV LLRYQQLIKE NLKEIAKLI TLEQGKTLAD AEGDVFRGLQ VVEHACSVTS LMMGETMPSI TKDMDLYSYR LPLGVCAGIA PFNFPAMIPL W MFPMAMVC ...String:
SSVPTVKLFI GGKFVESKSD KWIDIHNPAT NEVIGRVPQA TKAEMDAAIA SCKRAFPAWA DTSVLSRQQV LLRYQQLIKE NLKEIAKLI TLEQGKTLAD AEGDVFRGLQ VVEHACSVTS LMMGETMPSI TKDMDLYSYR LPLGVCAGIA PFNFPAMIPL W MFPMAMVC GNTFLMKPSE RVPGATMLLA KLLQDSGAPD GTLNIIHGQH EAVNFICDHP DIKAISFVGS NKAGEYIFER GS RHGKRVQ ANMGAKNHGV VMPDANKENT LNQLVGAAFG AAGQRCMALS TAVLVGEAKK WLPELVEHAK NLRVNAGDQP GAD LGPLIT PQAKERVCNL IDSGTKEGAS ILLDGRKIKV KGYENGNFVG PTIISNVKPN MTCYKEEIFG PVLVVLETET LDEA IQIVN NNPYGNGTAI FTTNGATARK YAHLVDVGQV GVNVPIPVPL PMFSFTGSRS SFRGDTNFYG KQGIQFYTQL KTITS QWKE EDATLSSPAV VMPTM

UniProtKB: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: alphafold 2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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