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- EMDB-61045: Cryo-EM structure of ALDH6A1-G446R -

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Basic information

Entry
Database: EMDB / ID: EMD-61045
TitleCryo-EM structure of ALDH6A1-G446R
Map data
Sample
  • Complex: ALDH6A1-G446R
    • Protein or peptide: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial
KeywordsALDH6A1 / G446R / 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: 3.0 Å
AuthorsSu G / Xu Y / Luan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Medicine Plus / Year: 2024
Title: Structural and biochemical basis for the pathogenic mutations of methylmalonate semialdehyde dehydrogenase ALDH6A1
Authors: Su G / Ju K / Xu Y / Jin Y / Chen L / Luan X
History
DepositionAug 1, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61045.png

Downloads & links

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Map

FileDownload / File: emd_61045.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.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.1
Minimum - Maximum-0.2748432 - 0.8730764
Average (Standard dev.)-0.0024071948 (±0.03729954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61045_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_61045_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-G446R

EntireName: ALDH6A1-G446R
Components
  • Complex: ALDH6A1-G446R
    • Protein or peptide: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial

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Supramolecule #1: ALDH6A1-G446R

SupramoleculeName: ALDH6A1-G446R / 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: 55.473637 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSSVPTVKL FIGGKFVESK SDKWIDIHNP ATNEVIGRVP QATKAEMDAA IASCKRAFPA WADTSVLSRQ QVLLRYQQLI KENLKEIAK LITLEQGKTL ADAEGDVFRG LQVVEHACSV TSLMMGETMP SITKDMDLYS YRLPLGVCAG IAPFNFPAMI P LWMFPMAM ...String:
MSSSVPTVKL FIGGKFVESK SDKWIDIHNP ATNEVIGRVP QATKAEMDAA IASCKRAFPA WADTSVLSRQ QVLLRYQQLI KENLKEIAK LITLEQGKTL ADAEGDVFRG LQVVEHACSV TSLMMGETMP SITKDMDLYS YRLPLGVCAG IAPFNFPAMI P LWMFPMAM VCGNTFLMKP SERVPGATML LAKLLQDSGA PDGTLNIIHG QHEAVNFICD HPDIKAISFV GSNKAGEYIF ER GSRHGKR VQANMGAKNH GVVMPDANKE NTLNQLVGAA FGAAGQRCMA LSTAVLVGEA KKWLPELVEH AKNLRVNAGD QPG ADLGPL ITPQAKERVC NLIDSGTKEG ASILLDGRKI KVKGYENGNF VGPTIISNVK PNMTCYKEEI FGPVLVVLET ETLD EAIQI VNNNPYGNRT AIFTTNGATA RKYAHLVDVG QVGVNVPIPV PLPMFSFTGS RSSFRGDTNF YGKQGIQFYT QLKTI TSQW KEEDATLSSP AVVMPTMGRE NLYFQ

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: 7.4
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296955
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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