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- EMDB-16540: Neurofascin isoform NF155 extracellular domain -

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Basic information

Entry
Database: EMDB / ID: EMD-16540
TitleNeurofascin isoform NF155 extracellular domain
Map dataVolume map of the NF155 extracellular domain obtained by negative stain EM.
Sample
  • Organelle or cellular component: Neurofascin isoform NF155
    • Protein or peptide: Neurofascin isoform NF155
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsMcKie SJ / Deane JE / Butt BG
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
University of Cambridge219447/Z/19/Z United Kingdom
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination.
Authors: Shannon J McKie / Alex S Nicholson / Emily Smith / Stuart Fawke / Eve R Caroe / James C Williamson / Benjamin G Butt / Denisa Kolářová / Ondřej Peterka / Michal Holčapek / Paul J Lehner ...Authors: Shannon J McKie / Alex S Nicholson / Emily Smith / Stuart Fawke / Eve R Caroe / James C Williamson / Benjamin G Butt / Denisa Kolářová / Ondřej Peterka / Michal Holčapek / Paul J Lehner / Stephen C Graham / Janet E Deane /
Abstract: Myelin is a multilayered membrane that tightly wraps neuronal axons, enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma ...Myelin is a multilayered membrane that tightly wraps neuronal axons, enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma membrane proteins and lipids, and disruption of these contacts causes devastating demyelinating diseases. Using two cell-based models of demyelinating sphingolipidoses, we demonstrate that altered lipid metabolism changes the abundance of specific plasma membrane proteins. These altered membrane proteins have known roles in cell adhesion and signaling, with several implicated in neurological diseases. The cell surface abundance of the adhesion molecule neurofascin (NFASC), a protein critical for the maintenance of myelin-axon contacts, changes following disruption to sphingolipid metabolism. This provides a direct molecular link between altered lipid abundance and myelin stability. We show that the NFASC isoform NF155, but not NF186, interacts directly and specifically with the sphingolipid sulfatide via multiple binding sites and that this interaction requires the full-length extracellular domain of NF155. We demonstrate that NF155 adopts an S-shaped conformation and preferentially binds sulfatide-containing membranes in , with important implications for protein arrangement in the tight axon-myelin space. Our work links glycosphingolipid imbalances to disturbance of membrane protein abundance and demonstrates how this may be driven by direct protein-lipid interactions, providing a mechanistic framework to understand the pathogenesis of galactosphingolipidoses.
#1: Journal: BioRxiv / Year: 2022
Title: Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination
Authors: McKie SJ / Deane JE / Nicholson A / Smith E / Fawke S / Caroe E / Williamson JC / Butt BG / Kolarova D / Peterka O / Holcapek M / Lehner PJ / Graham SC
History
DepositionJan 25, 2023-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16540.png

Downloads & links

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Map

FileDownload / File: emd_16540.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume map of the NF155 extracellular domain obtained by negative stain EM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 150 pix.
= 496.5 Å		3.31 Å/pix.
x 150 pix.
= 496.5 Å		3.31 Å/pix.
x 150 pix.
= 496.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.63
Minimum - Maximum-1.5165315 - 10.707807
Average (Standard dev.)6.421854e-05 (±0.4087378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 496.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map of the NF155 extracellular domain...

Fileemd_16540_half_map_1.map
AnnotationEM half map of the NF155 extracellular domain obtained by negative stain EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map of the NF155 extracellular domain...

Fileemd_16540_half_map_2.map
AnnotationEM half map of the NF155 extracellular domain obtained by negative stain EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Neurofascin isoform NF155

EntireName: Neurofascin isoform NF155
Components
  • Organelle or cellular component: Neurofascin isoform NF155
    • Protein or peptide: Neurofascin isoform NF155

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Supramolecule #1: Neurofascin isoform NF155

SupramoleculeName: Neurofascin isoform NF155 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Full length extracellular domain of neurofascin isoform NF155
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Neurofascin isoform NF155

MacromoleculeName: Neurofascin isoform NF155 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IEIPMDLTQP PTITKQSAKD HIVDPRDNIL IECEAKGNPA PSFHWTRNSR FFNIAKDPRV SMRRRSGTLV IDFRSGGRPE EYEGEYQCFA RNKFGTALSN RIRLQVSKSP LWPKENLDPV VVQEGAPLTL QCNPPPGLPS PVIFWMSSSM EPITQDKRVS QGHNGDLYFS ...String:
IEIPMDLTQP PTITKQSAKD HIVDPRDNIL IECEAKGNPA PSFHWTRNSR FFNIAKDPRV SMRRRSGTLV IDFRSGGRPE EYEGEYQCFA RNKFGTALSN RIRLQVSKSP LWPKENLDPV VVQEGAPLTL QCNPPPGLPS PVIFWMSSSM EPITQDKRVS QGHNGDLYFS NVMLQDMQTD YSCNARFHFT HTIQQKNPFT LKVLTNHPYN DSSLRNHPDM YSARGVAERT PSFMYPQGTA SSQMVLRGMD LLLECIASGV PTPDIAWYKK GGDLPSDKAK FENFNKALRI TNVSEEDSGE YFCLASNKMG SIRHTISVRV KAAPYWLDEP KNLILAPGED GRLVCRANGN PKPTVQWMVN GEPLQSAPPN PNREVAGDTI IFRDTQISSR AVYQCNTSNE HGYLLANAFV SVLDVPPRML SPRNQLIRVI LYNRTRLDCP FFGSPIPTLR WFKNGQGSNL DGGNYHVYEN GSLEIKMIRK EDQGIYTCVA TNILGKAENQ VRLEVKDPTR IYRMPEDQVA RRGTTVQLEC RVKHDPSLKL TVSWLKDDEP LYIGNRMKKE DDSLTIFGVA ERDQGSYTCV ASTELDQDLA KAYLTVLGRP DRPRDLELTD LAERSVRLTW IPGDANNSPI TDYVVQFEED QFQPGVWHDH SKYPGSVNSA VLRLSPYVNY QFRVIAINEV GSSHPSLPSE RYRTSGAPPE SNPGDVKGEG TRKNNMEITW TPMNATSAFG PNLRYIVKWR RRETREAWNN VTVWGSRYVV GQTPVYVPYE IRVQAENDFG KGPEPESVIG YSGEDYPRAA PTEVKVRVMN STAISLQWNR VYSDTVQGQL REYRAYYWRE SSLLKNLWVS QKRQQASFPG DRLRGVVSRL FPYSNYKLEM VVVNGRGDGP RSETKEFTTP EGVPSAPRRF RVRQPNLETI NLEWDHPEHP NGIMIGYTLK YVAFNGTKVG KQIVENFSPN QTKFTVQRTD PVSRYRFTLS ARTQVGSGEA VTEESPAPPN EATPTAAYTN NQADIATQGK HHHHHH

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.0023 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate
DetailsThis sample was highly pure and monodisperse

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20528
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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