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- EMDB-65430: Cryo-EM structure of the cage-top domain of the erlin1/2 complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-65430
TitleCryo-EM structure of the cage-top domain of the erlin1/2 complex purified using DDM and GDN
Map data
Sample
  • Complex: erlin1/2_DDM_GDN_C-terminus
KeywordsCryo-EM / complex / SPFH protein family / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYan L / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92354306 China
CitationJournal: Mol Cell / Year: 2026
Title: The Erlin1/2 complex is a dynamic scaffold for membrane microdomain assembly on the endoplasmic reticulum.
Authors: Lu Yan / Zihong Xu / Yuanhang Yao / Tadsanee Awang / Xiaoting Wang / Yonglun Wang / Chengying Ma / Ningning Li / Chen Song / Xiao-Wei Chen / Ning Gao /
Abstract: The SPFH (stomatin, prohibitin, flotillin, and HflK/C) family proteins are proposed scaffolds for organizing functional membrane microdomains (FMMs) on various cellular membranes. Erlin1 and Erlin2, ...The SPFH (stomatin, prohibitin, flotillin, and HflK/C) family proteins are proposed scaffolds for organizing functional membrane microdomains (FMMs) on various cellular membranes. Erlin1 and Erlin2, two endoplasmic reticulum (ER)-residing SPFH members, as heteromeric complexes, participate in ER-associated protein degradation (ERAD). However, the mechanisms underlying Erlin-mediated FMM organization and ERAD regulation remain poorly understood. Here, through cryoelectron microscopy (cryo-EM), we find that the human Erlin1/2 complex forms a 26-mer cage assembly, defining a nanometer-sized microdomain on the luminal leaflet. The intramembrane region of each subunit constitutes a specific phosphatidylinositol-binding pocket. ER proteins can be recruited to both the interior and exterior of these cages. By caging cargoes, the Erlin1/2 complex physically secludes them from their substrates or binding partners, conferring another layer of regulation on their functions. Moreover, individual cages can cluster to organize FMMs of different sizes. These dynamic properties underscore a general regulatory role of Erlin1/2 in various ER-related biological processes, including coronaviral replication.
History
DepositionJul 19, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65430.png

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Map

FileDownload / File: emd_65430.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336.64 Å		1.05 Å/pix.
x 320 pix.
= 336.64 Å		1.05 Å/pix.
x 320 pix.
= 336.64 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
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Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.03286744 - 0.06531541
Average (Standard dev.)0.00006053703 (±0.0028245978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65430_msk_1.map
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Additional map: #1

Fileemd_65430_additional_1.map
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Half map: #1

Fileemd_65430_half_map_1.map
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Half map: #2

Fileemd_65430_half_map_2.map
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Sample components

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Entire : erlin1/2_DDM_GDN_C-terminus

EntireName: erlin1/2_DDM_GDN_C-terminus
Components
  • Complex: erlin1/2_DDM_GDN_C-terminus

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Supramolecule #1: erlin1/2_DDM_GDN_C-terminus

SupramoleculeName: erlin1/2_DDM_GDN_C-terminus / type: complex / ID: 1 / Parent: 0
Details: Cage-Top structure of erlin1/2 complex purified with DDM and GDN
Source (natural)Organism: Homo sapiens (human)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25074
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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