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- EMDB-65382: Cryo-EM structure of the erlin1/2 complex purified using DDM and GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-65382
TitleCryo-EM structure of the erlin1/2 complex purified using DDM and GDN
Map data
Sample
  • Complex: The erlin1/2 complex
    • Protein or peptide: Erlin-1
    • Protein or peptide: Erlin-2
KeywordsCryo-EM / complex / MEMBRANE PROTEIN / SPFH protein family
Function / homology
Function and homology information


regulation of cholesterol biosynthetic process / Signaling by plasma membrane FGFR1 fusions / SREBP signaling pathway / negative regulation of cholesterol biosynthetic process / negative regulation of fatty acid biosynthetic process / cholesterol binding / cholesterol metabolic process / ERAD pathway / Signaling by FGFR1 in disease / Defective CFTR causes cystic fibrosis ...regulation of cholesterol biosynthetic process / Signaling by plasma membrane FGFR1 fusions / SREBP signaling pathway / negative regulation of cholesterol biosynthetic process / negative regulation of fatty acid biosynthetic process / cholesterol binding / cholesterol metabolic process / ERAD pathway / Signaling by FGFR1 in disease / Defective CFTR causes cystic fibrosis / ABC-family protein mediated transport / membrane raft / ubiquitin protein ligase binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Erlin1/2 / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 15, 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_65382.png

Downloads & links

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Map

FileDownload / File: emd_65382.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 504.96 Å		1.05 Å/pix.
x 480 pix.
= 504.96 Å		1.05 Å/pix.
x 480 pix.
= 504.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-0.722902 - 28.404098999999999
Average (Standard dev.)0.034564342 (±0.592636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 504.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The erlin1/2 complex

EntireName: The erlin1/2 complex
Components
  • Complex: The erlin1/2 complex
    • Protein or peptide: Erlin-1
    • Protein or peptide: Erlin-2

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Supramolecule #1: The erlin1/2 complex

SupramoleculeName: The erlin1/2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Erlin-1

MacromoleculeName: Erlin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.46184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARVLVAAVVG LVAVLLYASI HKIEEGHLAV YYRGGALLTS PSGPGYHIML PFITTFRSVQ TTLQTDEVKN VPCGTSGGVM IYIDRIEVV NMLAPYAVFD IVRNYTADYD KTLIFNKIHH ELNQFCSAHT LQEVYIELFD QIDENLKQAL QKDLNLMAPG L TIQAVRVT ...String:
ARVLVAAVVG LVAVLLYASI HKIEEGHLAV YYRGGALLTS PSGPGYHIML PFITTFRSVQ TTLQTDEVKN VPCGTSGGVM IYIDRIEVV NMLAPYAVFD IVRNYTADYD KTLIFNKIHH ELNQFCSAHT LQEVYIELFD QIDENLKQAL QKDLNLMAPG L TIQAVRVT KPKIPEAIRR NFELMEAEKT KLLIAAQKQK VVEKEAETER KKAVIEAEKI AQVAKIRFQQ KVMEKETEKR IS EIEDAAF LAREKAKADA EYYAAHKYAT SNKHKLTPEY LELKKYQAIA SNSKIYFGSN IPNMFVD

UniProtKB: Erlin-1

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Macromolecule #2: Erlin-2

MacromoleculeName: Erlin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.188473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LGAVVAVASS FFCASLFSAV HKIEEGHIGV YYRGGALLTS TSGPGFHLML PFITSYKSVQ TTLQTDEVKN VPCGTSGGVM IYFDRIEVV NFLVPNAVYD IVKNYTADYD KALIFNKIHH ELNQFCSVHT LQEVYIELFD QIDENLKLAL QQDLTSMAPG L VIQAVRVT ...String:
LGAVVAVASS FFCASLFSAV HKIEEGHIGV YYRGGALLTS TSGPGFHLML PFITSYKSVQ TTLQTDEVKN VPCGTSGGVM IYFDRIEVV NFLVPNAVYD IVKNYTADYD KALIFNKIHH ELNQFCSVHT LQEVYIELFD QIDENLKLAL QQDLTSMAPG L VIQAVRVT KPNIPEAIRR NYELMESEKT KLLIAAQKQK VVEKEAETER KKALIEAEKV AQVAEITYGQ KVMEKETEKK IS EIEDAAF LAREKAKADA ECYTAMKIAE ANKLKLTPEY LQLMKYKAIA SNSKMYFGKD IPNMFMD

UniProtKB: Erlin-2

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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

Concentration10 mg/mL
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: 2.6 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

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