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- EMDB-16931: NAPE-PLD dimer bound to a nanodisc -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16931
TitleNAPE-PLD dimer bound to a nanodisc
Map data
Sample
  • Complex: NAPE-PLD bound to a nanodisc
KeywordsNAPE-PLD / Lipid / Membrane / nanodisc / LIPID BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsChaves-Sanjuan A / Garau G / Bolognesi M
Funding support Italy, 1 items
OrganizationGrant numberCountry
Italian Ministry of HealthSB2D-CNI-BGU Italy
CitationJournal: To Be Published
Title: NAPE-PLD bound to a nanodisc
Authors: Chaves-Sanjuan A / Garau G / Bolognesi M
History
DepositionMar 29, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16931.png

Downloads & links

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Map

FileDownload / File: emd_16931.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.04 Å		0.89 Å/pix.
x 360 pix.
= 320.04 Å		0.89 Å/pix.
x 360 pix.
= 320.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.18183602 - 1.0821947
Average (Standard dev.)0.0014977551 (±0.053556494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16931_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_16931_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 : NAPE-PLD bound to a nanodisc

EntireName: NAPE-PLD bound to a nanodisc
Components
  • Complex: NAPE-PLD bound to a nanodisc

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Supramolecule #1: NAPE-PLD bound to a nanodisc

SupramoleculeName: NAPE-PLD bound to a nanodisc / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42 KDa

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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

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris
100.0 mMNaClNaCl
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: incubated on grid for 60 s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2500 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 214527
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.3) / Software - details: homogeneus refinement / Number images used: 8927
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.0.3) / Software - details: homogeneus refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.3)
FSC plot (resolution estimation)

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