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- EMDB-67393: Hemoglobin amyloid fibril - PM2 -

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Basic information

Entry
Database: EMDB / ID: EMD-67393
TitleHemoglobin amyloid fibril - PM2
Map data
Sample
  • Complex: Hemoglobin amyloid fibril - PM2
    • Protein or peptide: Hemoglobin subunit beta
Keywordsprotein fibril
Function / homology
Function and homology information


Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / erythrocyte development / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi S / Cao Q / Cao Y
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)National Key R&D Program of China. Grant Number: 2024YFF1106604 China
National Natural Science Foundation of China (NSFC)32372270 China
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Nano Lett / Year: 2026
Title: Structural Basis of Hemoglobin Amyloid Fibrils Revealed by cryo-EM and Molecular Dynamics Simulations.
Authors: Saiya Li / Xihua Liu / Shuangjian Li / Haoyun Yi / Yapeng Fang / Qin Cao / Yiping Cao /
Abstract: Hemoglobin has recently gained attention as a potential building block for amyloid-based biomaterials. However, the lack of atomic-level structural information has hindered its rational engineering. ...Hemoglobin has recently gained attention as a potential building block for amyloid-based biomaterials. However, the lack of atomic-level structural information has hindered its rational engineering. Here, we present atomic structures of hemoglobin amyloid fibrils determined by cryo-electron microscopy (cryo-EM). The structure of a new polymorph (PM2), together with the previously reported PM1, reveals that hemoglobin fibrillization is driven by the β-subunit. Using virtual fitting and molecular dynamics simulations, we demonstrate that the homologous α-subunit cannot adopt the amyloid fold due to steric clashes and electrostatic incompatibilities under acidic conditions (pH 2.0), particularly the introduction of positively charged histidine residues within the amyloid core. In contrast, the β-subunit forms stable fibrils, as its sequence enables favorable hydrophobic packing and electrostatic compatibility. Our findings thus provide the atomic-level explanation for subunit-specific amyloid formation in hemoglobin and establish a structural foundation for designing nanomaterials from this widely available agricultural byproduct.
History
DepositionDec 2, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67393.png

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Map

FileReleased
Projections & slices

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AxesX (Sec.)Y (Row.)Z (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-16.994668999999998 - 18.640408000000001
Average (Standard dev.)-0.000000000000944 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67393_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_67393_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67393_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hemoglobin amyloid fibril - PM2

EntireName: Hemoglobin amyloid fibril - PM2
Components
  • Complex: Hemoglobin amyloid fibril - PM2
    • Protein or peptide: Hemoglobin subunit beta

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Supramolecule #1: Hemoglobin amyloid fibril - PM2

SupramoleculeName: Hemoglobin amyloid fibril - PM2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Hemoglobin subunit beta

MacromoleculeName: Hemoglobin subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 15.977382 KDa
SequenceString:
MLTAEEKAAV TAFWGKVKVD EVGGEALGRL LVVYPWTQRF FESFGDLSTA DAVMNNPKVK AHGKKVLDSF SNGMKHLDDL KGTFAALSE LHCDKLHVDP ENFKLLGNVL VVVLARNFGK EFTPVLQADF QKVVAGVANA LAHRYH

UniProtKB: Hemoglobin subunit beta

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration20 mg/mL
BufferpH: 2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.391 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.218 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 36979
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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