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- EMDB-62333: cryo-EM structure of lipase/ligand/substrate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62333
Titlecryo-EM structure of lipase/ligand/substrate complex
Map data
Sample
  • Complex: complex of lipase and ligand
    • Protein or peptide: Patatin
  • Ligand: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Keywordslipase / HYDROLASE
Function / homology: / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / lipid catabolic process / hydrolase activity / Patatin
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLu DF / Zhu DY / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: cryo-EM structure of lipase/ligand/substrate complex
Authors: Lu DF / Zhu DY / Liu S
History
DepositionNov 9, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62333.png

Downloads & links

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Map

FileDownload / File: emd_62333.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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2612514 - 2.340869
Average (Standard dev.)0.005276041 (±0.08450071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62333_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_62333_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 : complex of lipase and ligand

EntireName: complex of lipase and ligand
Components
  • Complex: complex of lipase and ligand
    • Protein or peptide: Patatin
  • Ligand: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: complex of lipase and ligand

SupramoleculeName: complex of lipase and ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: Patatin

MacromoleculeName: Patatin / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Acinetobacter baumannii' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A4Q7ABV3.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 37.583746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKFQILALS GGGYRGLFTA TVLKELEQEA KENGHDSIAD CFDLITGTSV GGIVALAIAY GIKVEAIVDL FKSHGDKIFQ PKPFLKFTG SKYSNESLKT VLEEWFGDSI LGDLKCPVVI PTIDFTRGSP VTLKTPHNPN LKRDWKLKIV DVALATSAAP T YFPRHPIG ...String:
MEKFQILALS GGGYRGLFTA TVLKELEQEA KENGHDSIAD CFDLITGTSV GGIVALAIAY GIKVEAIVDL FKSHGDKIFQ PKPFLKFTG SKYSNESLKT VLEEWFGDSI LGDLKCPVVI PTIDFTRGSP VTLKTPHNPN LKRDWKLKIV DVALATSAAP T YFPRHPIG PNEYVDGGLF ANDPSLIGLH EADYMFKKNI QDVHILSIGT LSSKKQLNPS TKKDGGYLDW GEGSILKAAP NI IDLVLSS QQQFMEQMVK HRMEPFPNQF YKIDEQIVQA SAQFIGLDET SDAAKQVLEG NGIQSAKVAL GKDFIRNYFN QPS RKREWF DGPQKNVGGD KLNG

UniProtKB: Patatin

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Macromolecule #2: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-...

MacromoleculeName: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2- ...Name: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
type: ligand / ID: 2 / Number of copies: 6 / Formula: 4BW
Molecular weightTheoretical: 674.411 Da
Chemical component information

ChemComp-4BW:
2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one

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Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 6 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 548926
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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