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- EMDB-79135: Cryo EM structure of a formate acetyltransferase (PFL) from Fanny... -

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Basic information

Entry
Database: EMDB / ID: EMD-79135
TitleCryo EM structure of a formate acetyltransferase (PFL) from Fannyhessea vaginae in complex with CoA
Map data
Sample
  • Complex: tetramer of formate acetyltransferase (PFL)
    • Protein or peptide: Formate acetyltransferase
  • Ligand: COENZYME A
KeywordsSSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / formate acetyltransferase (PFL) / Fannyhessea vaginae / LYASE
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
Similarity search - Domain/homology
Formate acetyltransferase
Similarity search - Component
Biological speciesFannyhessea vaginae DSM 15829 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLiu L / Lovell S / Hammons AM / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2 items
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 Fannyhessea vaginae in complex with CoA
Authors: Liu L / Lovell S / Hammons AM
History
DepositionSep 17, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79135.png

Downloads & links

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Map

FileDownload / File: emd_79135.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-0.20207767 - 0.5982205
Average (Standard dev.)-0.00091900746 (±0.022198528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_79135_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_79135_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_79135_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tetramer of formate acetyltransferase (PFL)

EntireName: tetramer of formate acetyltransferase (PFL)
Components
  • Complex: tetramer of formate acetyltransferase (PFL)
    • Protein or peptide: Formate acetyltransferase
  • Ligand: COENZYME A

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Supramolecule #1: tetramer of formate acetyltransferase (PFL)

SupramoleculeName: tetramer of formate acetyltransferase (PFL) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Fannyhessea vaginae DSM 15829 (bacteria)
Molecular weightTheoretical: 333.89 KDa

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Macromolecule #1: Formate acetyltransferase

MacromoleculeName: Formate acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: formate C-acetyltransferase
Source (natural)Organism: Fannyhessea vaginae DSM 15829 (bacteria)
Molecular weightTheoretical: 83.473141 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHMG TLEAQTQGPG SMKEAWRGFT GGEWTHLIDV RDFIQKNYTP YEGDESFLAG PTEATTKLWA EVMDLFKQER EHGGVLDMD TKIVSTITSH PAGYIDKPYE KIVGLQTDKP LKRALMPNGG IRMAVSACKS YGYEVDPDLV KFYTDRRKTH N AGVFDVYT ...String:
MAHHHHHHMG TLEAQTQGPG SMKEAWRGFT GGEWTHLIDV RDFIQKNYTP YEGDESFLAG PTEATTKLWA EVMDLFKQER EHGGVLDMD TKIVSTITSH PAGYIDKPYE KIVGLQTDKP LKRALMPNGG IRMAVSACKS YGYEVDPDLV KFYTDRRKTH N AGVFDVYT PEMRACRHSH IITGLPDAYG RGRIIGDYRR LALYGLDRLI EEKEEEKANT HTTMDEETIR HREELSEQIR AL KEVNVMA GEYGFDVSKP AQNFKEAVQW LYFAYLASVK EQNGAAMSFG RTSTFLDIYA QRDLQEGTIT ESEVQEIIDH LVM KLRMVK FARTPEYNAL FSGDPQWVTE SIGGIGIDGR PMVTKNSFRF LHTLENMGTS PEPNLTVLWS TRLPEPFKRY CAKI SITTS SIQYENDDLM RVYHGDDYAI ACCVSSMVVG KEMQFFGARA NLAKCLLYAI NGGRDEITGE QIGPRFRPVE GDYLD YDDV IQKYRDMVYW LVSVYVNALN VIHYMHDKYA YERIQMAFHD EHIHRWFATG IAGLSVVADS LSAIKYAKVK VIRDET GLV TDFKIEGDYP KYGNDDDRVD SIARDVVEYF MKQIRKFNCY RNAVSTTSVL TITSNVVYGE KTGNTPDGRR AGTPFAP GA NPMHQRDTHG AVASLASVSK LPFRDAEDGI SNTFSIVPAA LGKSGNVMFG ECDMCEMKEL DDVSKIDFKT VDFTIENK P DCACAADASA KEGCEDNK

UniProtKB: Formate acetyltransferase

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Macromolecule #2: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 2 / Number of copies: 4 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Pressure: 0.005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5872 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsThe selected images were high-pass filtered and normalized
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

38lb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 2295925
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-38td:
Cryo EM structure of a formate acetyltransferase (PFL) from Fannyhessea vaginae in complex with CoA

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