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- PDB-38pa: Cryo EM structure of a formate acetyltransferase (PFL) from Amygd... -

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Basic information

Entry
Database: PDB / ID: 38pa
TitleCryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus in complex with CoA
ComponentsFormate acetyltransferase
KeywordsLYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / formate acetyltransferase (PFL) / Amygdalobacter nucleatus
Function / homology
Function and homology information


formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / cytosol
Similarity search - Function
Formate acetyltransferase / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain profile. / Glycine radical domain
Similarity search - Domain/homology
COENZYME A / Formate acetyltransferase
Similarity search - Component
Biological speciesAmygdalobacter nucleatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLiu, L. / Lovell, S. / Hammons, A.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD036339 United States
CitationJournal: To be published
Title: Cryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus in complex with CoA
Authors: Liu, L. / Lovell, S. / Hammons, A.M.
History
DepositionSep 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 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: Formate acetyltransferase
B: Formate acetyltransferase
C: Formate acetyltransferase
D: Formate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,2308
Polymers310,1594
Non-polymers3,0704
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Formate acetyltransferase / Pyruvate formate-lyase


Mass: 77539.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amygdalobacter nucleatus (bacteria) / Gene: HMPREF1872_00650 / Plasmid: AmnuA.20507.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A133YEC5, formate C-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tetramer of formate acetyltransferase (PFL) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.31016 MDa / Experimental value: YES
Source (natural)Organism: Amygdalobacter nucleatus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Cell: BL21(DE3) / Plasmid: AmnuA.20507.a.A1
Buffer solutionpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
SpecimenConc.: 0.5 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 2mM CoA and pyruvate added to the protein prior to grid preparation
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: VITRIFIED ICE
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal magnification: 100000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 400 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7387
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC5particle selection
4cryoSPARC5CTF correction
7UCSF ChimeraX1.12model fitting
9cryoSPARC5initial Euler assignment
10cryoSPARC5classification
11cryoSPARC53D reconstruction
12PHENIX2.2.1_6174model refinementDensity for residues L592-P619 was present in this CoA bound model but at a lower contour. Therefore, a 0.145V contour level is recommended. These residues were not observed in the apo structure 38LA even at a low contour level.
Image processingDetails: The selected images were high-pass filtered and normalized
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2847760 / Num. of class averages: 87 / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 38LA

38la


Accession code: 38LA / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00220456
ELECTRON MICROSCOPYf_angle_d0.36827684
ELECTRON MICROSCOPYf_dihedral_angle_d7.8152912
ELECTRON MICROSCOPYf_chiral_restr0.0362964
ELECTRON MICROSCOPYf_plane_restr0.0033600

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