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- PDB-9k8t: Cryo-EM structure of HE30 polymorph 2 -

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Basic information

Entry
Database: PDB / ID: 9k8t
TitleCryo-EM structure of HE30 polymorph 2
ComponentsNinjurin-1
KeywordsPROTEIN FIBRIL / helical fibril
Function / homology
Function and homology information


ferroptosis / pyroptotic cell death / membrane destabilizing activity / cytolysis / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / tissue regeneration / muscle cell differentiation ...ferroptosis / pyroptotic cell death / membrane destabilizing activity / cytolysis / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / tissue regeneration / muscle cell differentiation / cellular hyperosmotic response / heterotypic cell-cell adhesion / synaptic membrane / lipopolysaccharide binding / protein homooligomerization / positive regulation of angiogenesis / positive regulation of inflammatory response / 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 / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXia, W.C. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: ACS Nano / Year: 2025
Title: Amyloid Fibrillation of a Ninjurin-1-Derived α-Helical Peptide: Structural Insights into Conformational Transition.
Authors: Meijiao Wang / Wencheng Xia / Dan Zhao / Zhaoyi Zhai / Rongjing Chen / Xue Bai / Zhe Zhang / Hao Fan / Jian-Ping Zhang / Cong Liu / Fang Jiao /
Abstract: Amyloid fibrils, defined by their cross-β architecture, are central to both disease and function, yet the molecular principles governing their formation remain incompletely understood. Ninjurin-1 ...Amyloid fibrils, defined by their cross-β architecture, are central to both disease and function, yet the molecular principles governing their formation remain incompletely understood. Ninjurin-1 (NINJ1), a membrane protein essential for plasma membrane rupture (PMR) during cell death, contains an N-terminal amphipathic α-helix. Here, we investigate a key peptide fragment of this region (residues 40-69, HE30) and uncover its membrane-disruptive activity, self-assembly, and structural transitions. Monomeric HE30 reorganizes lipids to induce membrane thinning while undergoing an environmentally responsive α-helix-to-β-sheet transition that drives amyloid fibril formation. Fibrils formed at physiological temperatures are predominantly nontwisted, but elevated temperatures induce left-handed twisted structures with variable pitches and lengths, and even result in high-order superhelical bundles. We further resolved the twisted fibril structures of HE30 by cryo-EM, revealing two distinct fibril polymorphs stabilized by both hydrophobic and electrostatic interactions. Consistently, salts inhibit HE30 fibrillation, emphasizing the role of electrostatic interactions in stabilizing fibrils. Moreover, acidic conditions (∼pH 4.4) promote fibril formation, whereas alkaline conditions lead to disassembly into α-helical monomers in a reversible manner. AFM tracking reveals the asymmetric growth of fibrils, where one end elongates faster and the opposite end exhibits slower growth or complete inhibition. Functionally, HE30 fibrils are nontoxic and act as scaffolds for the temperature-controlled assembly of gold nanoparticle (AuNPs) superstructures. These findings not only advance our understanding of NINJ1-induced PMR but also provide a detailed structural basis for HE30 fibril formation via α-helix to β-sheet transitions and underscore their potential as building blocks for fibril-based biomaterials.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 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: Ninjurin-1
B: Ninjurin-1
C: Ninjurin-1
D: Ninjurin-1
E: Ninjurin-1
F: Ninjurin-1
G: Ninjurin-1
H: Ninjurin-1
I: Ninjurin-1
J: Ninjurin-1
K: Ninjurin-1
L: Ninjurin-1


Theoretical massNumber of molelcules
Total (without water)38,33712
Polymers38,33712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Ninjurin-1 / HE30 / hNINJ1 / Nerve injury-induced protein 1


Mass: 3194.721 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92982
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of HE30 polymorph 2 / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.16 ° / Axial rise/subunit: 2.34 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145228 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041932
ELECTRON MICROSCOPYf_angle_d0.9082586
ELECTRON MICROSCOPYf_dihedral_angle_d11.4131254
ELECTRON MICROSCOPYf_chiral_restr0.044354
ELECTRON MICROSCOPYf_plane_restr0.002312

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