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Yorodumi- PDB-8d45: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d45 | ||||||
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Title | Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase | ||||||
Components | Betaine--homocysteine S-methyltransferase 1 | ||||||
Keywords | HYDROLASE / betaine-homocysteine methyltransferase / BHSMT | ||||||
Function / homology | Function and homology information regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation ...regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation / zinc ion binding / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å | ||||||
Authors | Lyu, M. / Yu, E.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase Authors: Lyu, M. / Yu, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d45.cif.gz | 486.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d45.ent.gz | 410.6 KB | Display | PDB format |
PDBx/mmJSON format | 8d45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/8d45 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/8d45 | HTTPS FTP |
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-Related structure data
Related structure data | 27175MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45059.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BHMT / Production host: Homo sapiens (human) References: UniProt: Q93088, betaine-homocysteine S-methyltransferase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Betaine-Homocysteine Methyltransferase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 38.75 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471301 / Symmetry type: POINT | ||||||||||||||||||||||||
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