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Yorodumi- EMDB-38758: Structural of methylmalonate semialdehyde dehydrogenase ALDH6A1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38758 | |||||||||
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Title | Structural of methylmalonate semialdehyde dehydrogenase ALDH6A1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | dehydrogenase / ALDH6A1 / HYDROLASE | |||||||||
Function / homology | Function and homology information thymine metabolic process / valine 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 ...thymine metabolic process / valine 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Su G / Xu Y / Luan X | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structural and biochemical basis of methylmalonate semialdehyde dehydrogenase ALDH6A1 Authors: Su G / Xu Y / Luan X | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38758.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-38758-v30.xml emd-38758.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_38758.png | 48.9 KB | ||
Filedesc metadata | emd-38758.cif.gz | 5.1 KB | ||
Others | emd_38758_half_map_1.map.gz emd_38758_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38758 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38758 | HTTPS FTP |
-Validation report
Summary document | emd_38758_validation.pdf.gz | 889.3 KB | Display | EMDB validaton report |
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Full document | emd_38758_full_validation.pdf.gz | 888.8 KB | Display | |
Data in XML | emd_38758_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_38758_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38758 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38758 | HTTPS FTP |
-Related structure data
Related structure data | 8xxqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38758.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38758_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38758_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ALDH6A1
Entire | Name: ALDH6A1 |
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Components |
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-Supramolecule #1: ALDH6A1
Supramolecule | Name: ALDH6A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [...
Macromolecule | Name: 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) |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.146129 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 model | Type of model: OTHER / Details: alphafold 2 model |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200000 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |