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- PDB-9vvg: Cryo-EM structure of the erlin1/2 complex purified using GDN and CHS -

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Basic information

Entry
Database: PDB / ID: 9vvg
TitleCryo-EM structure of the erlin1/2 complex purified using GDN and CHS
Components
  • Erlin-1
  • Erlin-2
KeywordsMEMBRANE PROTEIN / Cryo-EM / complex / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYan, L. / Xu, Z. / Gao, N.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erlin-1
a: Erlin-2
M: Erlin-1
m: Erlin-2
L: Erlin-1
K: Erlin-1
k: Erlin-2
l: Erlin-2
J: Erlin-1
I: Erlin-1
i: Erlin-2
H: Erlin-1
G: Erlin-1
g: Erlin-2
h: Erlin-2
j: Erlin-2
C: Erlin-1
B: Erlin-1
b: Erlin-2
c: Erlin-2
F: Erlin-1
f: Erlin-2
E: Erlin-1
D: Erlin-1
d: Erlin-2
e: Erlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)889,11852
Polymers878,08426
Non-polymers11,03426
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Erlin-1 / Endoplasmic reticulum lipid raft-associated protein 1 / Protein KE04 / Stomatin-prohibitin- ...Endoplasmic reticulum lipid raft-associated protein 1 / Protein KE04 / Stomatin-prohibitin-flotillin-HflC/K domain-containing protein 1 / SPFH domain-containing protein 1


Mass: 33779.988 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERLIN1, C10orf69, KE04, KEO4, SPFH1 / Production host: Homo sapiens (human) / References: UniProt: O75477
#2: Protein
Erlin-2 / Endoplasmic reticulum lipid raft-associated protein 2 / Stomatin-prohibitin-flotillin-HflC/K domain- ...Endoplasmic reticulum lipid raft-associated protein 2 / Stomatin-prohibitin-flotillin-HflC/K domain-containing protein 2 / SPFH domain-containing protein 2


Mass: 33764.922 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERLIN2, C8orf2, SPFH2, UNQ2441/PRO5003/PRO9924 / Production host: Homo sapiens (human) / References: UniProt: O94905
#3: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1The erlin1/2 complexCOMPLEXThe erlin1/2 complex purified using GDN and CHS#1-#20RECOMBINANT
2erlin1COMPLEX#11RECOMBINANT
3erlin2COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 2100 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36885 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00363466
ELECTRON MICROSCOPYf_angle_d0.56285644
ELECTRON MICROSCOPYf_dihedral_angle_d6.1039558
ELECTRON MICROSCOPYf_chiral_restr0.0399958
ELECTRON MICROSCOPYf_plane_restr0.00510803

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