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

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Basic information

Entry
Database: PDB / ID: 9vvj
TitleCryo-EM structure of the erlin1/2 complex purified using DDM and GDN
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 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: 2.6 Å
AuthorsYan, L. / 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: Yan, L. / Gao, N.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
F: Erlin-1
f: Erlin-2
E: Erlin-1
D: Erlin-1
d: Erlin-2
C: Erlin-1
B: Erlin-1
b: Erlin-2
c: Erlin-2
e: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)903,48852
Polymers892,45426
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: 34461.840 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: 34188.473 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

ComponentName: The erlin1/2 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25074 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00364480
ELECTRON MICROSCOPYf_angle_d0.53387048
ELECTRON MICROSCOPYf_dihedral_angle_d6.5349805
ELECTRON MICROSCOPYf_chiral_restr0.03910179
ELECTRON MICROSCOPYf_plane_restr0.00410972

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