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- EMDB-79027: Cryo EM structure of a formate acetyltransferase (PFL) from Amygd... -

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Basic information

Entry
Database: EMDB / ID: EMD-79027
TitleCryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus 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) / Amygdalobacter nucleatus / 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 profile. / Glycine radical domain
Similarity search - Domain/homology
Formate acetyltransferase
Similarity search - Component
Biological speciesAmygdalobacter nucleatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 Amygdalobacter nucleatus in complex with CoA
Authors: Liu L / Lovell S / Hammons AM
History
DepositionSep 10, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79027.png

Downloads & links

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Map

FileDownload / File: emd_79027.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: 0.145
Minimum - Maximum-0.2613431 - 0.70929253
Average (Standard dev.)-0.0018958722 (±0.025466485)
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_79027_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_79027_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_79027_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: Amygdalobacter nucleatus (bacteria)
Molecular weightTheoretical: 310.16 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: Amygdalobacter nucleatus (bacteria)
Molecular weightTheoretical: 77.539859 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHMG TLEAQTQGPG SMEAYRSFKK GHWMDTIDVR DFIQHNYTPY EGDDSFLEGP TEATNQLWSQ VMELNKQEAA KGGVLDADT KIVSTITSHG PGYLNKDLEK IVGFQTDKPF KRSLQPFGGI RMAESALSAY GYTIDPEVEE IFTKYRKTHN Q GVFDAYTP ...String:
MAHHHHHHMG TLEAQTQGPG SMEAYRSFKK GHWMDTIDVR DFIQHNYTPY EGDDSFLEGP TEATNQLWSQ VMELNKQEAA KGGVLDADT KIVSTITSHG PGYLNKDLEK IVGFQTDKPF KRSLQPFGGI RMAESALSAY GYTIDPEVEE IFTKYRKTHN Q GVFDAYTP EMKAARHCGI ITGLPDAYGR GRIIGDYRRV ALYGIDRLIE DKKEQLHILE APTMTADIIR DREEISEQIR AL DEMAQMA ATYGFDIRRP AETAQEAIQW LYFAYLSAVK EQNGAAMSLG RTSTFLDIYI QRDLEEGRIT EKEAQEFMDH FVM KLRLVK FMRTPEYNDL FSGDPTWVTE SIGGMGIDGR TLVTKNSFRV LHTLSNLGPA PEPNLTVLWS PRLPIGFRRF CAKT SINTS SIQYESDELM RAEMFDDYAI ACCVSSMRVG KEMQFFGARA NLAKCLLYAI NGGMDEKKKM QVAPKFAPIT SEYLD YDEV MEKYTQMMEW LAGLYVNALN IIHYMHDKYC YERSEMALHD RVVKRYFATG IAGLSVVADS LSAIKYAKVK PIRDED GVA VDFEIEGDFP KYGNNDDRVD LIAAHLVSTF MNMIRKHHTY RNSIPTMSIL TITSNVVYGK KTGTTPDGRR AGQPFAP GA NPMHGRDSNG ALASLESVAK LPYSDSRDGI SNTFSLVPNS LGKED

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
Sugar embeddingMaterial: VITRIFIED ICE
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / 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
Details2mM CoA and pyruvate added to the protein prior to grid preparation

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
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: 7387 / 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 / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 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:

38la

Final reconstructionNumber classes used: 87 / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 2847760
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

Initial modelPDB ID:

38la


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.12)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-38pa:
Cryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus in complex with CoA

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