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- EMDB-57198: Structural basis of autoantibody binding in IgLON5 disease -

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Basic information

Entry
Database: EMDB / ID: EMD-57198
TitleStructural basis of autoantibody binding in IgLON5 disease
Map data
Sample
  • Complex: IgLON5 dimer with 2 Fabs
    • Protein or peptide: IgLON family member 5
    • Protein or peptide: antibody light chain
    • Protein or peptide: antibody heavy chain
Keywordsautoantibodies / neuronal adhesion molecule / IgCAM / IgLON / MEMBRANE PROTEIN
Function / homology
Function and homology information


neuron recognition / heterophilic cell-cell adhesion / regulation of synapse assembly / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IgLON family member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPerez L
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10005403 Switzerland
CitationJournal: To Be Published
Title: Structural basis of autoantibody binding in IgLON5 disease
Authors: Perez L
History
DepositionMar 13, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57198.png

Downloads & links

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Map

FileDownload / File: emd_57198.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 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: 0.1
Minimum - Maximum-1.3677636 - 1.6698952
Average (Standard dev.)-0.0000555981 (±0.011023133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 371.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_57198_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_57198_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 : IgLON5 dimer with 2 Fabs

EntireName: IgLON5 dimer with 2 Fabs
Components
  • Complex: IgLON5 dimer with 2 Fabs
    • Protein or peptide: IgLON family member 5
    • Protein or peptide: antibody light chain
    • Protein or peptide: antibody heavy chain

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Supramolecule #1: IgLON5 dimer with 2 Fabs

SupramoleculeName: IgLON5 dimer with 2 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IgLON family member 5

MacromoleculeName: IgLON family member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.581675 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VHVPARIVNI SSPVTVNEGG NVNLLCLAVG RPEPTVTWRQ LRDGFTSEGE ILEISDIQRG QAGEYECVTH NGVNSAPDSR RVLVTVNY

UniProtKB: IgLON family member 5

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Macromolecule #2: antibody light chain

MacromoleculeName: antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.609279 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SNYLAWYQQK PGQPPRLLIY GASSRAAGIA DRFRGSGSGT DFTLTISRLE PEDFAVYLC QLYVTSQGYT FGPGTRVDVK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SNYLAWYQQK PGQPPRLLIY GASSRAAGIA DRFRGSGSGT DFTLTISRLE PEDFAVYLC QLYVTSQGYT FGPGTRVDVK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLRSPVT KSFNRGEC

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Macromolecule #3: antibody heavy chain

MacromoleculeName: antibody heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.320324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLRLQESGPG LLKPSETLSL TCTVSGGSIS DSNHYWGWIR QPPGKGLEWI GSIYFSGSTY YNPSLRSRVT ISIATSNNQF SLRLPSLTA ADTAVYYCAR DVRRMFGATC FDYWGQGAVV TISSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QLRLQESGPG LLKPSETLSL TCTVSGGSIS DSNHYWGWIR QPPGKGLEWI GSIYFSGSTY YNPSLRSRVT ISIATSNNQF SLRLPSLTA ADTAVYYCAR DVRRMFGATC FDYWGQGAVV TISSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK

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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

Concentration1.2 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3169956
CTF correctionSoftware: (Name: cryoSPARC, MotionCorr2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dle

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 702836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50 / Avg.num./class: 3000 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

6dle

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 73.92
Output model

PDB-29in:
Structural basis of autoantibody binding in IgLON5 disease

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