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- PDB-27wm: horse myoglobin amyloid fibril - PM2 -

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Basic information

Entry
Database: PDB / ID: 27wm
Titlehorse myoglobin amyloid fibril - PM2
ComponentsMyoglobin
KeywordsPROTEIN FIBRIL
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / skeletal muscle contraction / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / skeletal muscle contraction / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Biological speciesEquus caballus (horse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi, S. / Cao, Q. / Cao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32572505 China
CitationJournal: Nano Lett / Year: 2026
Title: Myoglobin Amyloid Fibrils Reveal a Hierarchical Principle of Polymorphism and Electrostatic Self-Assembly.
Authors: Saiya Li / Shuangjian Li / Yiguo Zhao / Yapeng Fang / Qin Cao / Yiping Cao /
Abstract: The atomic architecture of apomyoglobin amyloid fibrils, despite the protein's dual distinction as the first structurally resolved protein and the paradigmatic nondisease amyloid, has remained a ...The atomic architecture of apomyoglobin amyloid fibrils, despite the protein's dual distinction as the first structurally resolved protein and the paradigmatic nondisease amyloid, has remained a decades-long puzzle. Here, we identify electrostatic screening as the critical switch that enables the formation of highly ordered apomyoglobin fibrils, allowing us to determine the cryo-electron microscopy structures of three distinct polymorphs (PM1, PM2, and PM3) at 2.7 Å resolution. The structures reveal a conserved "hydrophobic-in, positively charged-out" architecture, where a charged surface surrounds a tightly packed core, providing a structural explanation for salt-dependent assembly. Structural comparisons reveal a hierarchical principle of amyloid organization, in which short sequence segments retain conserved local conformations dictated by their intrinsic folding propensities, while variations in supramolecular packing give rise to polymorphic diversity. These findings establish a molecular framework for understanding electrostatically controlled self-assembly and the structural basis of amyloid polymorphism.
History
DepositionJun 15, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jul 29, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
C: Myoglobin
D: Myoglobin
E: Myoglobin
F: Myoglobin
G: Myoglobin
H: Myoglobin
I: Myoglobin
J: Myoglobin
K: Myoglobin
L: Myoglobin
M: Myoglobin
N: Myoglobin
O: Myoglobin


Theoretical massNumber of molelcules
Total (without water)48,58015
Polymers48,58015
Non-polymers00
Water00
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/peptide
Myoglobin / Nitrite reductase MB / Pseudoperoxidase MB


Mass: 3238.671 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Equus caballus (horse)
References: UniProt: P68082, Oxidoreductases; Acting on other nitrogenous compounds as donors, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
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: horse myoglobin amyloid fibril - PM2 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Equus caballus (horse)
Buffer solutionpH: 2
SpecimenConc.: 20 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.1067 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C1
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132690 / Symmetry type: HELICAL

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