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- EMDB-27175: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltran... -

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Basic information

Entry
Database: EMDB / ID: EMD-27175
TitleCryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase
Map data
Sample
  • Complex: Betaine-Homocysteine Methyltransferase
    • Protein or peptide: Betaine--homocysteine S-methyltransferase 1
Keywordsbetaine-homocysteine methyltransferase / BHSMT / HYDROLASE
Function / homology
Function and homology information


: / 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 ...: / 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
: / Betaine-homocysteine S-methyltransferase, BHMT / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile.
Similarity search - Domain/homology
Betaine--homocysteine S-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsLyu M / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase
Authors: Lyu M / Yu EW
History
DepositionJun 1, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27175.png

Downloads & links

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Map

FileDownload / File: emd_27175.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-2.78514 - 4.6541467
Average (Standard dev.)-0.000014157278 (±0.051604595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27175_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27175_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 : Betaine-Homocysteine Methyltransferase

EntireName: Betaine-Homocysteine Methyltransferase
Components
  • Complex: Betaine-Homocysteine Methyltransferase
    • Protein or peptide: Betaine--homocysteine S-methyltransferase 1

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Supramolecule #1: Betaine-Homocysteine Methyltransferase

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

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Macromolecule #1: Betaine--homocysteine S-methyltransferase 1

MacromoleculeName: Betaine--homocysteine S-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: betaine-homocysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.059441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 471301
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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