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- EMDB-35129: Acyl-ACP synthetase structure bound to pimelic acid monoethyl ester -

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Basic information

Entry
Database: EMDB / ID: EMD-35129
TitleAcyl-ACP synthetase structure bound to pimelic acid monoethyl ester
Map data
Sample
  • Complex: Acyl-ACP Synthetase bound to pimelic acid monoethyl ester
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: 7-ethoxy-7-oxidanylidene-heptanoic acid
KeywordsAcyl-ACP synthetase / Tool enzyme / CYTOSOLIC PROTEIN
Function / homologyligase activity, forming carbon-sulfur bonds / : / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Acyl-acyl carrier protein synthetase
Function and homology information
Biological speciesVibrio harveyi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsHuang H / Wang C / Chang S / Cui T / Xu Y / Zhang H / Zhou C / Zhang X / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32125003 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Structure and catalytic mechanism of exogenous fatty acid recycling by AasS, a versatile acyl-ACP synthetase
Authors: Huang H / Wang C / Chang S / Cui T / Xu Y / Zhang H / Zhou C / Zhang X / Feng Y
History
DepositionJan 13, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35129.png

Downloads & links

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Map

FileDownload / File: emd_35129.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 330 pix.
= 306.9 Å		0.93 Å/pix.
x 330 pix.
= 306.9 Å		0.93 Å/pix.
x 330 pix.
= 306.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5204642 - 2.9333751
Average (Standard dev.)0.0011728657 (±0.06551629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 306.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35129_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35129_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 : Acyl-ACP Synthetase bound to pimelic acid monoethyl ester

EntireName: Acyl-ACP Synthetase bound to pimelic acid monoethyl ester
Components
  • Complex: Acyl-ACP Synthetase bound to pimelic acid monoethyl ester
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: 7-ethoxy-7-oxidanylidene-heptanoic acid

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Supramolecule #1: Acyl-ACP Synthetase bound to pimelic acid monoethyl ester

SupramoleculeName: Acyl-ACP Synthetase bound to pimelic acid monoethyl ester
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio harveyi (bacteria)

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Macromolecule #1: Acyl-acyl carrier protein synthetase

MacromoleculeName: Acyl-acyl carrier protein synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio harveyi (bacteria)
Molecular weightTheoretical: 60.496258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNQYVNDPSN YQLLIKNLLF SPVAFNPEQE IVYANHRRHS YKTFHDRVRQ FANALTKMGV KKGDTVAVMD YDSHRYLECY FAIPMIGAK LHMINVRLSP EQILYTIDHA EDDIILIHEE FLPILDQIKG RIDTVTRYVV LRDDEECEYE RLLEQESTEY N FPDFDENT ...String:
MNQYVNDPSN YQLLIKNLLF SPVAFNPEQE IVYANHRRHS YKTFHDRVRQ FANALTKMGV KKGDTVAVMD YDSHRYLECY FAIPMIGAK LHMINVRLSP EQILYTIDHA EDDIILIHEE FLPILDQIKG RIDTVTRYVV LRDDEECEYE RLLEQESTEY N FPDFDENT VATTFYTTGT TGFPKGVFFT HRQLVLHTMG ILSTIGTNAS QGRLHQGDIY MPITPMFHVH AWGLPYMATM LG VKQVYPG KYVPDVLLNL IEQEKVTFSH CVPTILHLLL SSPKSKAMDF SGWKVVIGGA ALPKALCKSA LERDIDVFAG YGM SETGPI LSIVQLTPEQ LELDVDQQAE YRSKTGKKVA LVEAYIVDED MNKLPHDGET AGEIVVRAPW LTPNYYKDNK NSKA LWRGG YLHTGDVAHI DDEGFIKITD RVKDMIKISG EWVSSLELED ILHQHQSVSE VAVIGMPHNK WGEVPLALVT LKEDA QVTE KELLGFAKDF INKGILAREA LLLKVKIVDE IAKTSVGKVD KKELRKLHL

UniProtKB: Acyl-acyl carrier protein synthetase

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Macromolecule #2: 7-ethoxy-7-oxidanylidene-heptanoic acid

MacromoleculeName: 7-ethoxy-7-oxidanylidene-heptanoic acid / type: ligand / ID: 2 / Number of copies: 6 / Formula: OBK
Molecular weightTheoretical: 188.221 Da
Chemical component information

ChemComp-OBK:
7-ethoxy-7-oxidanylidene-heptanoic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 510518
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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