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- EMDB-78899: Cryo EM structure of a formate acetyltransferase (PFL) from Amygd... -

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Basic information

Entry
Database: EMDB / ID: EMD-78899
TitleCryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus
Map data
Sample
  • Complex: tetramer of formate acetyltransferase (PFL)
    • Protein or peptide: Formate acetyltransferase
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 / Resolution: 2.74 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/Office of the DirectorS10OD036339 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Cryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus
Authors: Liu L / Lovell S / Hammons AM
History
DepositionSep 1, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78899.png

Downloads & links

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Map

FileDownload / File: emd_78899.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: 0.061
Minimum - Maximum-0.08018739 - 0.23401019
Average (Standard dev.)-0.00042418408 (±0.0071127554)
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_78899_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_78899_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_78899_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

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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: all
Source (natural)Organism: Amygdalobacter nucleatus (bacteria)
Molecular weightTheoretical: 310 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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Experimental details

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Structure determination

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: VITREOUS 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

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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: 7532 / 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
Particle selectionNumber selected: 16303831
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AF-A0A133YEC5-F1
Final reconstructionNumber classes used: 22 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 1558198
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:

5-f1


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

PDB-38la:
Cryo EM structure of a formate acetyltransferase (PFL) from Amygdalobacter nucleatus

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