8D45 | pdb_00008d45

Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase

PDB DOI: https://doi.org/10.2210/pdb8D45/pdb
EM Map EMD-27175: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-06-01 Released: 2022-11-16
Deposition Author(s): Lyu, M., Yu, E.W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structure of human Kidney Betaine-Homocysteine Methyltransferase

Lyu, M., Yu, E.W.

To be published.

Macromolecule Content

Total Structure Weight: 180.24 kDa
Atom Count: 10,562
Modeled Residue Count: 1,358
Deposited Residue Count: 1,624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Betaine--homocysteine S-methyltransferase 1	A, B, C, D	406	Homo sapiens	Mutation(s): 0 Gene Names: BHMT EC: 2.1.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q93088 (Homo sapiens) Explore Q93088 Go to UniProtKB: Q93088
PHAROS: Q93088 GTEx: ENSG00000145692
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93088
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection
Version 1.2: 2025-05-28
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.