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Yorodumi- EMDB-27175: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltran... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27175 | |||||||||
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Title | Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | betaine-homocysteine methyltransferase / BHSMT / HYDROLASE | |||||||||
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 / extracellular exosome / zinc ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Lyu M / Yu EW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase Authors: Lyu M / Yu EW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27175.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-27175-v30.xml emd-27175.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27175_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_27175.png | 92.8 KB | ||
Filedesc metadata | emd-27175.cif.gz | 5 KB | ||
Others | emd_27175_half_map_1.map.gz emd_27175_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27175 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27175 | HTTPS FTP |
-Validation report
Summary document | emd_27175_validation.pdf.gz | 745.1 KB | Display | EMDB validaton report |
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Full document | emd_27175_full_validation.pdf.gz | 744.6 KB | Display | |
Data in XML | emd_27175_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_27175_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27175 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27175 | HTTPS FTP |
-Related structure data
Related structure data | 8d45MC 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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-Map
File | Download / File: emd_27175.map.gz / Format: CCP4 / Size: 103 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: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27175_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27175_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Betaine-Homocysteine Methyltransferase
Entire | Name: Betaine-Homocysteine Methyltransferase |
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Components |
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-Supramolecule #1: Betaine-Homocysteine Methyltransferase
Supramolecule | Name: Betaine-Homocysteine Methyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Betaine--homocysteine S-methyltransferase 1
Macromolecule | Name: Betaine--homocysteine S-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: betaine-homocysteine S-methyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.059441 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAVRQLH REFLRAGSNV MQTFTFYASE DKLENRGNY VLEKISGQEV NEAACDIARQ VADEGDALVA GGVSQTPSYL SCKSETEVKK VFLQQLEVFM KKNVDFLIAE Y FEHVEEAV ...String: MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAVRQLH REFLRAGSNV MQTFTFYASE DKLENRGNY VLEKISGQEV NEAACDIARQ VADEGDALVA GGVSQTPSYL SCKSETEVKK VFLQQLEVFM KKNVDFLIAE Y FEHVEEAV WAVETLIASG KPVAATMCIG PEGDLHGVPP GECAVRLVKA GASIIGVNCH FDPTISLKTV KLMKEGLEAA RL KAHLMSQ PLAYHTPDCN KQGFIDLPEF PFGLEPRVAT RWDIQKYARE AYNLGVRYIG GCCGFEPYHI RAIAEELAPE RGF LPPASE KHGSWGSGLD MHTKPWVRAR ARKEYWENLR IASGRPYNPS MSKPDGWGVT KGTAELMQQK EATTEQQLKE LFEK QKFKS Q UniProtKB: Betaine--homocysteine S-methyltransferase 1 |
-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 BIOQUANTUM (6k x 4k) / Average electron dose: 38.75 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |