[English] 日本語
Yorodumi
- EMDB-38758: Structural of methylmalonate semialdehyde dehydrogenase ALDH6A1 -

+
Open data


ID or keywords:

Loading...

-
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-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38758.png

Downloads & links

-
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)

Slices (1/2)

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 °

-
Supplemental data

-
Half map: #1

Fileemd_38758_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38758_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ALDH6A1

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

-
Supramolecule #1: ALDH6A1

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

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

+
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