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- EMDB-62668: Cryo-EM structure of the 3:3 LGI1-ADAM22 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62668
TitleCryo-EM structure of the 3:3 LGI1-ADAM22 complex
Map data
Sample
  • Complex: The 3:3 LGI1-ADAM22 complex
    • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 22
    • Protein or peptide: Leucine-rich glioma-inactivated protein 1
Keywordsepilepsy / syanapse / adam / eptp / wd40 / cell adhesion
Function / homology
Function and homology information


LGI-ADAM interactions / negative regulation of cell adhesion / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / central nervous system development / postsynaptic density membrane / metalloendopeptidase activity ...LGI-ADAM interactions / negative regulation of cell adhesion / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / central nervous system development / postsynaptic density membrane / metalloendopeptidase activity / neuron projection development / integrin binding / nervous system development / positive regulation of cell growth / cell adhesion / axon / signaling receptor binding / dendrite / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich glioma-inactivated , EPTP repeat / EAR / : / EPTP domain / EAR repeat profile. / ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. ...Leucine-rich glioma-inactivated , EPTP repeat / EAR / : / EPTP domain / EAR repeat profile. / ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / EGF-like domain, extracellular / EGF-like domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Metallopeptidase, catalytic domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / EGF-like domain signature 1. / EGF-like domain / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich glioma-inactivated protein 1 / Disintegrin and metalloproteinase domain-containing protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsYamaguchi T / Okatsu K / Kubota M / Mistumori A / Yamagata A / Fukai S
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Elife / Year: 2025
Title: Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22.
Authors: Yamaguchi T / Okatsu K / Kubota M / Mitsumori A / Yamagata A / Fukata Y / Fukata M / Shibata M / Fukai S
History
DepositionDec 11, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62668.png

Downloads & links

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Map

FileDownload / File: emd_62668.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 320 pix.
= 240.64 Å		0.75 Å/pix.
x 320 pix.
= 240.64 Å		0.75 Å/pix.
x 320 pix.
= 240.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.4700025 - 0.64984304
Average (Standard dev.)-0.0006204148 (±0.015292313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 240.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62668_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_62668_additional_1.map
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Half map: #2

Fileemd_62668_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62668_half_map_2.map
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Sample components

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Entire : The 3:3 LGI1-ADAM22 complex

EntireName: The 3:3 LGI1-ADAM22 complex
Components
  • Complex: The 3:3 LGI1-ADAM22 complex
    • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 22
    • Protein or peptide: Leucine-rich glioma-inactivated protein 1

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Supramolecule #1: The 3:3 LGI1-ADAM22 complex

SupramoleculeName: The 3:3 LGI1-ADAM22 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Disintegrin and metalloproteinase domain-containing protein 22

MacromoleculeName: Disintegrin and metalloproteinase domain-containing protein 22
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.80323 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NVEEETKYIE LMIVNDHLMF KKHRLSVVHT NTYAKSVVNM ADLIYKDQLK TRIVLVAMET WATDNKFAIS ENPLITLREF MKYRRDFIK EKSDAVHLFS GSQFESSRSG AAYIGGICSL LKGGGVNEFG KTDLMAVTLA QSLAHNIGII SDKRKLASGE C KCEDTWSG ...String:
NVEEETKYIE LMIVNDHLMF KKHRLSVVHT NTYAKSVVNM ADLIYKDQLK TRIVLVAMET WATDNKFAIS ENPLITLREF MKYRRDFIK EKSDAVHLFS GSQFESSRSG AAYIGGICSL LKGGGVNEFG KTDLMAVTLA QSLAHNIGII SDKRKLASGE C KCEDTWSG CIMGDTGYYL PKKFTQCNIE EYHDFLNSGG GACLFNKPSK LLDPPECGNG FIETGEECDC GTPAECVLEG AE CCKKCTL TQDSQCSDGL CCKKCKFQPM GTVCREAVND CDIRETCSGN SSQCAPNIHK MDGYSCDGVQ GICFGGRCKT RDR QCKYIW GQKVTASDKY CYEKLNIEGT EKGNCGKDKD TWIQCNKRDV LCGYLLCTNI GNIPRLGELD GEITSTLVVQ QGRT LNCSG GHVKLEEDVD LGYVEDGTPC GPQMMCLEHR CLPVASFNFS TCLSSKEGTI CSGNGVCSNE LKCVCNRHWI GSDCN TYFP HNDDAKTGIT LSG

UniProtKB: Disintegrin and metalloproteinase domain-containing protein 22

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Macromolecule #2: Leucine-rich glioma-inactivated protein 1

MacromoleculeName: Leucine-rich glioma-inactivated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.570785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DAAQPARRAR RTYEAYPAKP KCPAVCTCTK DNALCENARS IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDD AFIGLPHLEY LFIENNNIKS ISRHTFRGLK SLIHLSLANN NLQTLPKDIF KGLDSLTNVD LRGNSFNCDC K LKWLVEWL ...String:
DAAQPARRAR RTYEAYPAKP KCPAVCTCTK DNALCENARS IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDD AFIGLPHLEY LFIENNNIKS ISRHTFRGLK SLIHLSLANN NLQTLPKDIF KGLDSLTNVD LRGNSFNCDC K LKWLVEWL GHTNATVEDI YCEGPPEYKK RKINSLSSKD FDCIITEFAK SQDLPYQSLS IDTFSYLNDE YVVIAQPFTG KC IFLEWDH VEKTFRNYDN ITGTSTVVCK PIVIETQLYV IVAQLFGGSH IYKRDSFANK FIKIQDIEIL KIRKPNDIET FKI ENNWYF VVADSSKAGF TTIYKWNGNG FYSHQSLHAW YRDTDVEYLE IVRTPQTLRT PHLILSSSSQ RPVIYQWNKA TQLF TNQTD IPNMEDVYAV KHFSVKGDVY ICLTRFIGDS KVMKWGGSSF QDIQAMPSRG SMVFQPLQIN NYQYAILGSD YSFTQ VYNW DAEKAKFVKF QELNVQAPRS FTHVSINKRN FLFASSFKGN TQIYKHVIVD LSAKHHHHHH

UniProtKB: Leucine-rich glioma-inactivated protein 1

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7625 / Average exposure time: 2.79627 sec. / Average electron dose: 60.8046 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9kzc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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