[English] 日本語
Yorodumi
- PDB-9qkv: Human myoferlin (1-1997) in complex with an MSP2N2 lipid nanodisc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qkv
TitleHuman myoferlin (1-1997) in complex with an MSP2N2 lipid nanodisc (15 mol% DOPS, 5 mol% Cholesterol)
ComponentsMyoferlin
KeywordsMEMBRANE PROTEIN / Ferlins / myoferlin / multi-C2 domains / lipid nanodisc
Function / homology
Function and homology information


regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / muscle contraction / phospholipid binding / caveola / centriolar satellite / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle ...regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / muscle contraction / phospholipid binding / caveola / centriolar satellite / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle / nuclear membrane / cilium / ciliary basal body / 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: 2.74 Å
AuthorsCretu, C. / Moser, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CR 937/2-1 and 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
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
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: The cytosolic domain of human myoferlin (residues 1-1997), cloned in-frame with a twin-StrepII affinity tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOF, FER1L3, KIAA1207 / Plasmid: pCC76
Details (production host): twin-StrepII-HRV3C-Myoferlin(1-1997)
Cell (production host): Sf9 cells / 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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human myoferlin (1-1997) in complex with an MSP2N2 lipid nanodisc (comprising 15 mol% DOPS, 5 mol% Cholesterol)
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 mM4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acidHEPES1
2200 mMpotassium chlorideKCl1
31.25 % (v/v)glycerolC3H8O31
41 mMTris(2-carboxyethyl)phosphine hydrochlorideTCEP1
50.5 mMcalcium chlorideCaCl21
SpecimenConc.: 0.77 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Prior to cryo-EM grid preparation, the sample was crosslinked with glutaraldehyde (0.05 % (v/v)) in batch and purified by size-exclusion chromatography
Specimen supportDetails: The grid was treated with the Plasma Cleaner (Harrick Plasma) for 1 min at medium settings, followed by vitrification in liquid ethane-propane (37%/63%), cooled by liquid nitrogen
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

-
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: 2000 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: 3.45 sec. / Electron dose: 39.85 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9800 / Details: 9621 movies were accepted after curation
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv.4.5particle selection
2PHENIX1.21.2_5419model refinement
3EPUv.3.6image acquisition
5cryoSPARCv.4.5CTF correction
10cryoSPARCv.4.5initial Euler assignment
11cryoSPARCv.4.5final Euler assignment
12RELIONv.5.0classification
13cryoSPARCv.4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2917286
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277729 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 135.43 / Protocol: AB INITIO MODEL / Space: REAL
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: 122.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004614101
ELECTRON MICROSCOPYf_angle_d0.92219108
ELECTRON MICROSCOPYf_chiral_restr0.05322040
ELECTRON MICROSCOPYf_plane_restr0.00742478
ELECTRON MICROSCOPYf_dihedral_angle_d7.10231896

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more