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- EMDB-70263: The Erlin1/2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70263
TitleThe Erlin1/2 complex
Map data
Sample
  • Complex: Complex of 13 Erlin1/2 heterodimers
    • Protein or peptide: Erlin-1
    • Protein or peptide: Erlin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSPFH / ER / Erlin1 / Erlin2 / 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: 3.0 Å
AuthorsGao J / Shao S
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70263.png

Downloads & links

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Map

FileDownload / File: emd_70263.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.6385877 - 1.001736
Average (Standard dev.)0.002133545 (±0.035818852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70263_additional_1.map
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Additional map: #2

Fileemd_70263_additional_2.map
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Half map: #1

Fileemd_70263_half_map_1.map
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Half map: #2

Fileemd_70263_half_map_2.map
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Sample components

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Entire : Complex of 13 Erlin1/2 heterodimers

EntireName: Complex of 13 Erlin1/2 heterodimers
Components
  • Complex: Complex of 13 Erlin1/2 heterodimers
    • Protein or peptide: Erlin-1
    • Protein or peptide: Erlin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of 13 Erlin1/2 heterodimers

SupramoleculeName: Complex of 13 Erlin1/2 heterodimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Erlin-1

MacromoleculeName: Erlin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.429402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSMTQAR VLVAAVVGLV AVLLYASIHK IEEGHLAVYY RGGALLTSPS GPGYHIMLP FITTFRSVQT TLQTDEVKNV PCGTSGGVMI YIDRIEVVNM LAPYAVFDIV RNYTADYDKT LIFNKIHHEL N QFCSAHTL ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSMTQAR VLVAAVVGLV AVLLYASIHK IEEGHLAVYY RGGALLTSPS GPGYHIMLP FITTFRSVQT TLQTDEVKNV PCGTSGGVMI YIDRIEVVNM LAPYAVFDIV RNYTADYDKT LIFNKIHHEL N QFCSAHTL QEVYIELFDQ IDENLKQALQ KDLNLMAPGL TIQAVRVTKP KIPEAIRRNF ELMEAEKTKL LIAAQKQKVV EK EAETERK KAVIEAEKIA QVAKIRFQQK VMEKETEKRI SEIEDAAFLA REKAKADAEY YAAHKYATSN KHKLTPEYLE LKK YQAIAS NSKIYFGSNI PNMFVDSSCA LKYSDIRTGR ESSLPSKEAL EPSGENVIQN KESTG

UniProtKB: Erlin-1

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Macromolecule #2: Erlin-2

MacromoleculeName: Erlin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.884473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQLGAVVAV ASSFFCASLF SAVHKIEEGH IGVYYRGGAL LTSTSGPGFH LMLPFITSYK SVQTTLQTDE VKNVPCGTSG GVMIYFDRI EVVNFLVPNA VYDIVKNYTA DYDKALIFNK IHHELNQFCS VHTLQEVYIE LFDQIDENLK LALQQDLTSM A PGLVIQAV ...String:
MAQLGAVVAV ASSFFCASLF SAVHKIEEGH IGVYYRGGAL LTSTSGPGFH LMLPFITSYK SVQTTLQTDE VKNVPCGTSG GVMIYFDRI EVVNFLVPNA VYDIVKNYTA DYDKALIFNK IHHELNQFCS VHTLQEVYIE LFDQIDENLK LALQQDLTSM A PGLVIQAV RVTKPNIPEA IRRNYELMES EKTKLLIAAQ KQKVVEKEAE TERKKALIEA EKVAQVAEIT YGQKVMEKET EK KISEIED AAFLAREKAK ADAECYTAMK IAEANKLKLT PEYLQLMKYK AIASNSKIYF GKDIPNMFMD SAGSVSKQFE GLA DKLSFG LEDEPLETAT KEN

UniProtKB: Erlin-2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.32 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95469
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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