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- PDB-39oz: Cryo-EM structure of glutamate mutase from Carboxydothermus hydro... -

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Basic information

Entry
Database: PDB / ID: 39oz
TitleCryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Components
  • Glutamate mutase epsilon subunit
  • Glutamate mutase sigma subunit
KeywordsISOMERASE / glutamate mutase / adenosylcobalamin / intact Co-C bond / pre-activation state / cryo-EM
Function / homology
Function and homology information


methylaspartate mutase / methylaspartate mutase activity / cobalamin binding / metal ion binding
Similarity search - Function
Glutamate mutase epsilon subunit / Glutamate mutase E subunit, C-terminal domain superfamily / Methylaspartate mutase E chain (MutE) / Glutamate mutase sigma subunit / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / Glutamate mutase epsilon subunit / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, X.Y. / Tjia-Fleck, S.K. / Tian, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM155016 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Authors: Zhang, X.Y. / Tjia-Fleck, S.K. / Tian, S.L.
History
DepositionOct 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate mutase epsilon subunit
B: Glutamate mutase epsilon subunit
C: Glutamate mutase sigma subunit
D: Glutamate mutase sigma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8707
Polymers137,0374
Non-polymers1,8333
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamate mutase epsilon subunit / Glutamate mutase E chain / Glutamate mutase large subunit / Methylaspartate mutase


Mass: 53632.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: mutE, glmE, CHY_0309 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AFA5, methylaspartate mutase
#2: Protein Glutamate mutase sigma subunit / Glutamate mutase S chain / Glutamate mutase small subunit / Methylaspartate mutase


Mass: 14886.253 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: glmS, mamA, CHY_0307 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AFA7, methylaspartate mutase
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: glutamate mutase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 57.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 509882
Details: Two local refinements were performed in cryoSPARC using gold-standard half-set separation. Corresponding half-maps from the two local refinements were combined separately in Phenix to ...Details: Two local refinements were performed in cryoSPARC using gold-standard half-set separation. Corresponding half-maps from the two local refinements were combined separately in Phenix to generate the final combined half-map pair.
Symmetry type: POINT

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