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- PDB-9h6x: Cryo-EM structure of lipid-bound human myoferlin (25 mol% DOPS/5 ... -

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Basic information

Entry
Database: PDB / ID: 9h6x
TitleCryo-EM structure of lipid-bound human myoferlin (25 mol% DOPS/5 mol% PI(4,5)P2 nanodisc)
ComponentsMyoferlin
KeywordsMEMBRANE PROTEIN / Ferlin / multi-C2 domain protein / tail-anchored membrane protein / vesicle docking and fusion / membrane remodeling
Function / homology
Function and homology information


regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / muscle contraction / caveola / phospholipid binding / centriolar satellite / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle ...regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / muscle contraction / caveola / phospholipid binding / centriolar satellite / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle / nuclear membrane / ciliary basal body / cilium / intracellular membrane-bounded organelle / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain ...Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain / Ferlin, first C2 domain / : / FerB (NUC096) domain / FerI (NUC094) domain / Ferlin C-terminus / Ferlin dsRNA-binding domain-like domain / FerB / FerI / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Myoferlin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsCretu, C. / Moser, T. / Preobraschenski, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CR 937/2-1, EXC 2067/1-390729940 Germany
CitationJournal: EMBO J / Year: 2025
Title: Structural insights into lipid membrane binding by human ferlins.
Authors: Constantin Cretu / Aleksandar Chernev / Csaba Zoltán Kibédi Szabó / Vladimir Pena / Henning Urlaub / Tobias Moser / Julia Preobraschenski /
Abstract: Ferlins are ancient membrane proteins with a unique architecture, and play central roles in crucial processes that involve Ca-dependent vesicle fusion. Despite their links to multiple human diseases ...Ferlins are ancient membrane proteins with a unique architecture, and play central roles in crucial processes that involve Ca-dependent vesicle fusion. Despite their links to multiple human diseases and numerous functional studies, a mechanistic understanding of how these multi-C domain-containing proteins interact with lipid membranes to promote membrane remodelling and fusion is currently lacking. Here we obtain near-complete cryo-electron microscopy structures of human myoferlin and dysferlin in their Ca- and lipid-bound states. We show that ferlins adopt compact, ring-like tertiary structures upon membrane binding. The top arch of the ferlin ring, composed of the CC-CD region, is rigid and exhibits only little variability across the observed functional states. In contrast, the N-terminal CB and the C-terminal CF-CG domains cycle between alternative conformations and, in response to Ca, close the ferlin ring, promoting tight interaction with the target membrane. Probing key domain interfaces validates the observed architecture, and informs a model of how ferlins engage lipid bilayers in a Ca-dependent manner. This work reveals the general principles of human ferlin structures and provides a framework for future analyses of ferlin-dependent cellular functions and disease mechanisms.
History
DepositionOct 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Myoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,93813
Polymers232,6261
Non-polymers1,31212
Water00
1


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

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Components

#1: Protein Myoferlin / Fer-1-like protein 3


Mass: 232625.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fer-1-like protein 3, FER1L3, MYOF / Source: (gene. exp.) Homo sapiens (human) / Gene: MYOF, FER1L3, KIAA1207 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NZM1
#2: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE


Mass: 455.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34NO10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Soluble human myoferlin (residues 1-1997) bound to an MSP2N2-based lipid nanodisc (comprising 25 mol% DOPS and 5 mol% PI(4,5)P2)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
2200 mMpotassium chlorideKCl1
30.5 mMcalcium chlorideCaCl21
42.5 %GlycerolC3H8O31
51 mMDithiothreitolDTT1
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The myoferlin-nanodisc complex was assembled in vitro, crosslinked with 0.07% (v/v) glutaraldehyde, and purified by size-exclusion chromatography on Superose 6 10/300 prior to cryo-EM grid preparation
Specimen supportDetails: Plasma Cleaner model PDC-32G-2 (Harrick Plasma) / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 165000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.16 sec. / Electron dose: 39.595 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31039
Details: dataset 1: 8660 movies, 39.595 e-/A2 dataset 2: 22379 movies, 39.216 e-/A2
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.5particle selection
2EPUv3.6.0image acquisition
4cryoSPARCv4.5CTF correction
7UCSF ChimeraXv1.8model fitting
9cryoSPARCv4.5initial Euler assignment
10cryoSPARCv4.5final Euler assignment
11RELIONv5.0classification
12cryoSPARCv4.53D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7651843
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233637 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 152.37 / Protocol: OTHER / Space: REAL
Details: Iterative model building and refinement with ISOLDE, Coot, and Phenix (phenix.real_space_refine)
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 152.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003614150
ELECTRON MICROSCOPYf_angle_d0.790219173
ELECTRON MICROSCOPYf_chiral_restr0.04982043
ELECTRON MICROSCOPYf_plane_restr0.00692489
ELECTRON MICROSCOPYf_dihedral_angle_d5.65881898

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