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- PDB-8uip: Cryo-EM Structure of Human Ninjurin1 curved oligomer -

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Basic information

Entry
Database: PDB / ID: 8uip
TitleCryo-EM Structure of Human Ninjurin1 curved oligomer
ComponentsNinjurin-1
KeywordsIMMUNE SYSTEM / Ninjurin1 / NINJ1 / inflammation / inflammasome / pyroptosis / plasma membrane rupture
Function / homology
Function and homology information


cell adhesion mediator activity / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / muscle cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed cell death / heterotypic cell-cell adhesion / pyroptotic inflammatory response / synaptic membrane ...cell adhesion mediator activity / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / muscle cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed cell death / heterotypic cell-cell adhesion / pyroptotic inflammatory response / synaptic membrane / lipopolysaccharide binding / protein homooligomerization / positive regulation of inflammatory response / positive regulation of angiogenesis / nervous system development / angiogenesis / killing of cells of another organism / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDavid, L. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI139914 United States
CitationJournal: Cell / Year: 2024
Title: NINJ1 mediates plasma membrane rupture by cutting and releasing membrane disks.
Authors: Liron David / Jazlyn P Borges / L Robert Hollingsworth / Allen Volchuk / Isabelle Jansen / Evelyn Garlick / Benjamin E Steinberg / Hao Wu /
Abstract: The membrane protein NINJ1 mediates plasma membrane rupture in pyroptosis and other lytic cell death pathways. Here, we report the cryo-EM structure of a NINJ1 oligomer segmented from NINJ1 rings. ...The membrane protein NINJ1 mediates plasma membrane rupture in pyroptosis and other lytic cell death pathways. Here, we report the cryo-EM structure of a NINJ1 oligomer segmented from NINJ1 rings. Each NINJ1 subunit comprises amphipathic (⍺1, ⍺2) and transmembrane (TM) helices (⍺3, ⍺4) and forms a chain of subunits, mainly by the TM helices and ⍺1. ⍺3 and ⍺4 are kinked, and the Gly residues are important for function. The NINJ1 oligomer possesses a concave hydrophobic side that should face the membrane and a convex hydrophilic side formed by ⍺1 and ⍺2, presumably upon activation. This structural observation suggests that NINJ1 can form membrane disks, consistent with membrane fragmentation by recombinant NINJ1. Live-cell and super-resolution imaging uncover ring-like structures on the plasma membrane that are released into the culture supernatant. Released NINJ1 encircles a membrane inside, as shown by lipid staining. Therefore, NINJ1-mediated membrane disk formation is different from gasdermin-mediated pore formation, resulting in membrane loss and plasma membrane rupture.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ninjurin-1
B: Ninjurin-1
C: Ninjurin-1


Theoretical massNumber of molelcules
Total (without water)49,0713
Polymers49,0713
Non-polymers00
Water0
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 Ninjurin-1


Mass: 16356.998 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NINJ1 / Production host: Escherichia phage EcSzw_1 (virus) / References: UniProt: Q92982

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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: Ninjurin 1 ring oligomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia phage EcSzw_1 (virus)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626231 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE

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