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- EMDB-19474: N.meningitidis NadV3 surface expressed homotrimeric antigen structure -

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Basic information

Entry
Database: EMDB / ID: EMD-19474
TitleN.meningitidis NadV3 surface expressed homotrimeric antigen structure
Map dataN.meningitidis NadAV3 homotrimeric map
Sample
  • Organelle or cellular component: homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis
    • Other: NadAV3
Keywordsstructural vaccinology / bacterial antigen / autotransporter / CELL ADHESION
Biological speciesNeisseria meningitidis (bacteria) / Neisseria meningitidis serogroup B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.2 Å
AuthorsCalvaresi V / Dello Iacono L / Borghi S / Luzzi E / Biolchi A / Benucci B / Ferlenghi I / Peschiera I / Giusti F / Fontana LE ...Calvaresi V / Dello Iacono L / Borghi S / Luzzi E / Biolchi A / Benucci B / Ferlenghi I / Peschiera I / Giusti F / Fontana LE / Kan Z / Spinello Z / Merola M / Delany I / Rand KD / Norris N
Funding support Italy, 1 items
OrganizationGrant numberCountry
Other government675879 Italy
CitationJournal: To Be Published
Title: N.meningitidis NadV3 surface expressed homotrimeric antigen structure
Authors: Calvaresi V / Dello Iacono L / Borghi S / Luzzi E / Biolchi A / Benucci B / Ferlenghi I / Peschiera I / Giusti F / Fontana LE / Kan Z / Spinello Z / Merola M / Delany I / Rand KD / Norris N
History
DepositionJan 24, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19474.png

Downloads & links

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Map

FileDownload / File: emd_19474.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN.meningitidis NadAV3 homotrimeric map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 240 pix.
= 420. Å		1.75 Å/pix.
x 240 pix.
= 420. Å		1.75 Å/pix.
x 240 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00741
Minimum - Maximum-0.015418739 - 0.12839699
Average (Standard dev.)0.00006227523 (±0.0034690902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1 map for FSC

Fileemd_19474_half_map_1.map
Annotationhalf1 map for FSC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: helf2 map for FSC

Fileemd_19474_half_map_2.map
Annotationhelf2 map for FSC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homotrimeric coiled-coil FL NadA bacterial adhesin expressed on t...

EntireName: homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis
Components
  • Organelle or cellular component: homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis
    • Other: NadAV3

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Supramolecule #1: homotrimeric coiled-coil FL NadA bacterial adhesin expressed on t...

SupramoleculeName: homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: NadAV3 appendage generated
Source (natural)Organism: Neisseria meningitidis (bacteria) / Strain: B

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Macromolecule #1: NadAV3

MacromoleculeName: NadAV3 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
SequenceString: DDVKKAATVA IAAAYNNGQE INGFKAGETI YDIDEDGTIT KKDATAADVE ADDFKGLGL KKVVTNLTKT VNENKQNVDA KVKAAESEIE KLTTKLADTD A ALADTDAA LDATTNALNK LGENITTFAE ETKTNIVKID EKLEAASKHD DV KKAATVA IAAAYNNGQE ...String:
DDVKKAATVA IAAAYNNGQE INGFKAGETI YDIDEDGTIT KKDATAADVE ADDFKGLGL KKVVTNLTKT VNENKQNVDA KVKAAESEIE KLTTKLADTD A ALADTDAA LDATTNALNK LGENITTFAE ETKTNIVKID EKLEAASKHD DV KKAATVA IAAAYNNGQE INGFKAGETI YDIDEDGTIT KKDATAADVE ADD FKGLGL KKVVTNLTKT VNENKQNVDA KVKAAESEIE KLTTKLADTD AALA DTDAA LDATTNALNK LGENITTFAE ETKTNIVKID EKLEAASDDV KKAAT VAIA AAYNNGQEIN GFKAGETIYD IDEDGTITKK DATAADVEAD DFKGLG LKK VVTNLTKTVN ENKQNVDAKV KAAESEIEKL TTKLADTDAA LADTDAA LD ATTNALNKLG ENITTFAEET KTNIVKIDEK LEAAS
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.00 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMtris-HCLTris-HCL
150.0 mMNaClsodium chloride

Details: 20 mM Tris-HCL, 150 mM NaCl
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
Details: Quantifoil R2-2 grid, 400 mesh Cu, Electron Microscopy Sciences) was rendered hydrophilic with 15 mA current for 90 second by glow discharge in a EmiTech K100X
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Quantifoil R2-2 grid, 400 mesh Cu, Electron Microscopy Sciences) charged with 2.5 microliter of the specimens were deposited onto the grid and vitrified using a Mark IV Vitrobot with a ...Details: Quantifoil R2-2 grid, 400 mesh Cu, Electron Microscopy Sciences) charged with 2.5 microliter of the specimens were deposited onto the grid and vitrified using a Mark IV Vitrobot with a blotting time of 4 second and humidity of 100 at 277.15K.
Detailsthe sample was homogeneously distributed, no aggregation was observed. Original 1mg/ml NadAV3 sample was diluted up to 0.067 mg/ml for further EMM observations.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15273
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Xmipp
Details: the image processing has been performed within Scipion Software platform. The particles were classified several times to prune the set in 2D using Relion. Best classes obtained were used to ...Details: the image processing has been performed within Scipion Software platform. The particles were classified several times to prune the set in 2D using Relion. Best classes obtained were used to generate an initial model within EMAN2.
Number images used: 7327
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6eun


Chain - Residue range: 24-170 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: the initial model consisted of the complete biological assembly for PDB entry 6EUN
Detailsrigid-body fitting was done using ChimeraX. The position of rigid body fitted PDB 6EUN coordinates into the 3DEM map has been saved.Image of the rigid body fitting has been uploaded.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 0.4796 / Target criteria: cross-correlation coefficient

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