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- EMDB-35249: Acyl-ACP synthetase structure bound to C18:1-ACP -

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Basic information

Entry
Database: EMDB / ID: EMD-35249
TitleAcyl-ACP synthetase structure bound to C18:1-ACP
Map data
Sample
  • Complex: Acyl-ACP Synthetase bound to C18:1-ACP
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: 4'-PHOSPHOPANTETHEINE
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: OLEIC ACID
KeywordsAcyl-ACP synthetase / Tool enzyme / CYTOSOLIC PROTEIN / Ligase / TRANSPORT PROTEIN-CYTOSOLIC PROTEIN complex
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
Similarity search - Function
: / 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 carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. ...: / 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 carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein / Acyl-acyl carrier protein synthetase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 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: To Be Published
Title: Acyl-ACP synthetase structure bound to C18:1-ACP
Authors: Huang H / Wang C / Chang S / Cui T / Xu Y / Zhang H / Zhou C / Zhang X / Feng Y
History
DepositionFeb 4, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35249.png

Downloads & links

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Map

FileDownload / File: emd_35249.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-2.1535068 - 3.9399755
Average (Standard dev.)-0.0004893634 (±0.09602423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35249_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_35249_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 C18:1-ACP

EntireName: Acyl-ACP Synthetase bound to C18:1-ACP
Components
  • Complex: Acyl-ACP Synthetase bound to C18:1-ACP
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: 4'-PHOSPHOPANTETHEINE
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: OLEIC ACID

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Supramolecule #1: Acyl-ACP Synthetase bound to C18:1-ACP

SupramoleculeName: Acyl-ACP Synthetase bound to C18:1-ACP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio harveyi (bacteria)

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Macromolecule #1: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.64546 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGADSLDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGHQA

UniProtKB: Acyl carrier protein

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Macromolecule #2: Acyl-acyl carrier protein synthetase

MacromoleculeName: Acyl-acyl carrier protein synthetase / type: protein_or_peptide / ID: 2 / 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 #3: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 3 / Number of copies: 6 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE

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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #5: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 5 / Number of copies: 6 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC 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: GATAN K2 SUMMIT (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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299233
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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