20YJ | pdb_000020yj

Hemoglobin amyloid fibril - PM2

  • Classification: PROTEIN FIBRIL
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2025-12-02 Released: 2026-07-22 
  • Deposition Author(s): Li, S., Cao, Q., Cao, Y.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Hemoglobin Amyloid Fibrils Revealed by cryo-EM and Molecular Dynamics Simulations.

Li, S.Liu, X.Li, S.Yi, H.Fang, Y.Cao, Q.Cao, Y.

(2026) Nano Lett 26: 8867-8873

  • DOI: https://doi.org/10.1021/acs.nanolett.6c02217
  • Primary Citation Related Structures: 
    20YJ

  • PubMed 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. 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.


  • Organizational Affiliation
    • Department of Food Science & Engineering, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China.

Macromolecule Content 

  • Total Structure Weight: 159.77 kDa 
  • Atom Count: 2,590 
  • Modeled Residue Count: 330 
  • Deposited Residue Count: 1,450 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
145Bos taurusMutation(s): 0 
UniProt
Find proteins for P02070 (Bos taurus)
Explore P02070 
Go to UniProtKB:  P02070
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02070
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)ChinaNational Key R&D Program of China. Grant Number: 2024YFF1106604
National Natural Science Foundation of China (NSFC)China32372270
National Natural Science Foundation of China (NSFC)China32271276

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references