9SSV | pdb_00009ssv

Human Methionine Synthase With Methylcobalamin, Activation Domain From Full-Length


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9SSV

This is version 1.1 of the entry. See complete history

Literature

Structural insights into cobalamin loading and reactivation of human methionine synthase.

Ferreira, D.S.M.McLennan, K.Diamond, C.Vollmar, M.Kiyani, W.Froese, D.S.Kopec, J.Bailey, H.J.Chalk, R.Basle, A.Elkins, J.M.Coker, J.A.Yue, W.W.McCorvie, T.J.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-72899-3
  • Primary Citation Related Structures: 
    9SSP, 9SSQ, 9SSR, 9SSS, 9SST, 9SSU, 9SSV

  • PubMed Abstract: 

    Human methionine synthase (MTR) is an essential enzyme of one carbon metabolism. Consisting of a catalytic N-half and a cobalamin binding C-half, MTR utilises this intricate organometallic cofactor in the methyl transfer from methyltetrahydrofolate to homocysteine producing methionine. Cobalamin loading into MTR, and its subsequent activation, requires methylmalonic aciduria and homocystinuria Type D (MMADHC) protein and methionine synthase reductase (MTRR), respectively. However, the molecular basis of cobalamin binding and activation of human MTR aided by MMADHC and MTRR remains unknown. Here, using cryo-electron microscopy, we determine structures of human MTR in its apo, and cobalamin bound states. Apo MTR adopts a conformation where the two halves of the enzyme act independently with the C-half posed to bind cobalamin. Binding of cobalamin and its activation causes conformational changes in MTR that result in a flexible catalytically active state. AlphaFold predictions, validated by interaction studies, show that MMADHC interacts with the C-half of apo MTR to facilitate cobalamin loading. Unexpectedly we found that MTRR interacts at two distinct sites within the C-half of MTR which may aid in activation. Collectively these findings lay the groundwork to uncover the mechanisms through how MMADHC and MTRR coordinate cobalamin loading and activation of human MTR.


  • Organizational Affiliation
    • Nuffield Department of Clinical Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 140.7 kDa 
  • Atom Count: 2,716 
  • Modeled Residue Count: 338 
  • Deposited Residue Count: 1,265 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine synthase1,265Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99707
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092809/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Data collection, Database references