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- PDB-9o9u: The Erlin1/2 complex -

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Basic information

Entry
Database: PDB / ID: 9o9u
TitleThe Erlin1/2 complex
Components
  • Erlin-1
  • Erlin-2
KeywordsMEMBRANE PROTEIN / SPFH / ER / Erlin1 / Erlin2
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: 3 Å
AuthorsGao, J. / Shao, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG073277 United States
David and Lucile Packard Foundation United States
Richard and Susan Smith Family Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Structures of human organellar SPFH protein complexes.
Authors: Jingjing Gao / Dawafuti Sherpa / Nikita Kupko / Haruka Chino / Jianwei Zeng / Sichen Shao /
Abstract: Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric ...Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
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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
B: Erlin-1
b: Erlin-2
C: Erlin-1
c: Erlin-2
D: Erlin-1
d: Erlin-2
E: Erlin-1
e: Erlin-2
F: Erlin-1
f: Erlin-2
G: Erlin-1
g: Erlin-2
H: Erlin-1
h: Erlin-2
I: Erlin-1
i: Erlin-2
J: Erlin-1
j: Erlin-2
K: Erlin-1
k: Erlin-2
L: Erlin-1
l: Erlin-2
M: Erlin-1
m: Erlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,049,83252
Polymers1,044,08026
Non-polymers5,75126
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 42429.402 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: 37884.473 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: 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
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: Complex of 13 Erlin1/2 heterodimers / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 52.32 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95469 / Symmetry type: POINT

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