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- EMDB-65927: Cryo-EM structure of the human Erlin2 oligomer -

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Basic information

Entry
Database: EMDB / ID: EMD-65927
TitleCryo-EM structure of the human Erlin2 oligomer
Map data
Sample
  • Complex: Cryo-EM structure of the human Erlin2 oligomer
    • Protein or peptide: Erlin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsErlin2 oligomer / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsQian HW / Jia XX
Funding support1 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65927.png

Downloads & links

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Map

FileDownload / File: emd_65927.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 680 pix.
= 363.8 Å		0.54 Å/pix.
x 680 pix.
= 363.8 Å		0.54 Å/pix.
x 680 pix.
= 363.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.535 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0631
Minimum - Maximum-0.29157406 - 0.5425768
Average (Standard dev.)0.00045684716 (±0.016146163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 363.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65927_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_65927_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the human Erlin2 oligomer

EntireName: Cryo-EM structure of the human Erlin2 oligomer
Components
  • Complex: Cryo-EM structure of the human Erlin2 oligomer
    • Protein or peptide: Erlin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the human Erlin2 oligomer

SupramoleculeName: Cryo-EM structure of the human Erlin2 oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Erlin-2

MacromoleculeName: Erlin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.535357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SAVHKIEEGH IGVYYRGGAL LTSTSGPGFH LMLPFITSYK SVQTTLQTDE VKNVPCGTSG GVMIYFDRIE VVNFLVPNAV YDIVKNYTA DYDKALIFNK IHHELNQFCS VHTLQEVYIE LFDQIDENLK LALQQDLTSM APGLVIQAVR VTKPNIPEAI R RNYELMES ...String:
SAVHKIEEGH IGVYYRGGAL LTSTSGPGFH LMLPFITSYK SVQTTLQTDE VKNVPCGTSG GVMIYFDRIE VVNFLVPNAV YDIVKNYTA DYDKALIFNK IHHELNQFCS VHTLQEVYIE LFDQIDENLK LALQQDLTSM APGLVIQAVR VTKPNIPEAI R RNYELMES EKTKLLIAAQ KQKVVEKEAE TERKKALIEA EKVAQVAEIT YGQKVMEKET EKKISEIEDA AFLAREKAKA DA ECYTAMK IAEANKLKLT PEYLQLMKYK AIASNSKIYF GK

UniProtKB: Erlin-2

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 26 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 3471 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100060
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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