9SSP | pdb_00009ssp

Human Methionine Synthase With Methyltetrahydrofolate, N-Half From Full-Length

PDB DOI: https://doi.org/10.2210/pdb9SSP/pdb
EM Map EMD-55190: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-09-26 Released: 2025-10-15
Deposition Author(s): Ferreira, D.S.M., Yue, W.W., McCorvie, T.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into cobalamin loading and reactivation of human methionine synthase

Ferreira, D.S.M., Yue, W.W., McCorvie, T.J.

To be published.

Macromolecule Content

Total Structure Weight: 141.16 kDa
Atom Count: 4,925
Modeled Residue Count: 638
Deposited Residue Count: 1,265
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	1,265	Homo sapiens	Mutation(s): 0 Gene Names: MTR EC: 2.1.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q99707 (Homo sapiens) Explore Q99707 Go to UniProtKB: Q99707
PHAROS: Q99707 GTEx: ENSG00000116984
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99707
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THH (Subject of Investigation/LOI) Query on THH Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID C₂₀ H₂₅ N₇ O₆ ZNOVTXRBGFNYRX-STQMWFEESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	ISOLDE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Ferreira, D.S.M.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092809/Z/10/Z

Revision History (Full details and data files)

Version 1.0: 2025-10-15
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.