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- PDB-9wff: Cryo-EM structure of the human Erlin2 oligomer -

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Basic information

Entry
Database: PDB / ID: 9wff
TitleCryo-EM structure of the human Erlin2 oligomer
ComponentsErlin-2
KeywordsMEMBRANE PROTEIN / Erlin2 oligomer
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 proteins 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: 2.12 Å
AuthorsQian, H.W. / Jia, X.X.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J Mol Cell Biol / Year: 2026
Title: Structural insights into the organization of the human Erlin complex.
Authors: Xiaoxiao Jia / Guoyun Liu / Haiwen Li / Hongwu Qian /
Abstract: The endoplasmic reticulum (ER) lipid raft proteins (Erlins) belong to the stomatin-prohibitin-flotillin-HflC/K (SPFH) family and form highly oligomeric platforms that mediate the degradation of ...The endoplasmic reticulum (ER) lipid raft proteins (Erlins) belong to the stomatin-prohibitin-flotillin-HflC/K (SPFH) family and form highly oligomeric platforms that mediate the degradation of activated inositol 1,4,5-trisphosphate receptors by facilitating their interaction with the E3 ligase RNF170. However, the molecular mechanisms underlying this process remain unclear. Here, we successfully reconstituted the Erlin1-Erlin2 complex and its complex with RNF170 by overexpressing these components in HEK293F cells. We also isolated the Erlin2 oligomer by solely expressing Erlin2 in the cells. Using cryo-EM, we determined the structures of the Erlin1-Erlin2 complex, Erlin1-Erlin2-RNF170 complex, and Erlin2 oligomer at resolutions of 3.29 Å, 3.05 Å, and 2.12 Å, respectively. Both the Erlin1-Erlin2 complex and the Erlin2 oligomer exhibit similar cage-like architectures, with the Erlin1-Erlin2 complex containing 13 pairs of Erlin1 and Erlin2 subunits, whereas the Erlin2 oligomer comprises 26 Erlin2. Although RNF170 was clearly identified during protein purification, it was invisible in the final 3D reconstruction, suggesting a high degree of flexibility between RNF170 and the Erlin complex. Multiple water molecules were identified in the Erlin2 oligomer, underscoring their critical roles in facilitating the high degree of oligomerization of the Erlin2 complex. Taken together, our structural investigation elucidates the molecular basis for the assembly of the Erlin complex and provides a framework for further investigation.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Erlin-2
X: Erlin-2
A: Erlin-2
Z: Erlin-2
C: Erlin-2
B: Erlin-2
E: Erlin-2
D: Erlin-2
G: Erlin-2
F: Erlin-2
I: Erlin-2
H: Erlin-2
K: Erlin-2
J: Erlin-2
M: Erlin-2
L: Erlin-2
O: Erlin-2
N: Erlin-2
Q: Erlin-2
P: Erlin-2
S: Erlin-2
R: Erlin-2
U: Erlin-2
T: Erlin-2
W: Erlin-2
V: Erlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)825,67152
Polymers819,91926
Non-polymers5,75126
Water62,5303471
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-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: 31535.357 Da / Num. of mol.: 26
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
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3471 / Source method: isolated from a natural source / Formula: H2O
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

ComponentName: Cryo-EM structure of the human Erlin2 oligomer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100060 / Symmetry type: POINT
RefinementHighest resolution: 2.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049052
ELECTRON MICROSCOPYf_angle_d0.55812208
ELECTRON MICROSCOPYf_dihedral_angle_d11.4461220
ELECTRON MICROSCOPYf_chiral_restr0.0421416
ELECTRON MICROSCOPYf_plane_restr0.0041540

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