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- EMDB-64995: Hemoglobin amyloid fibril -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64995
TitleHemoglobin amyloid fibril
Map data
Sample
  • Complex: Hemoglobin amyloid fibril
    • 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: 3.26 Å
AuthorsLi S / Cao Q / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)National Key R&D Program of China (2024YFF1106604) China
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: To Be Published
Title: Structure of hemoglobin subunit beta (bovin) at 2.6 angstroms resolution
Authors: Li S / Cao Q / Cao Y
History
DepositionJun 9, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64995.png

Downloads & links

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Map

FileDownload / File: emd_64995.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-20.262936 - 32.659171999999998
Average (Standard dev.)-0.000000000000975 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64995_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64995_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64995_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hemoglobin amyloid fibril

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

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Supramolecule #1: Hemoglobin amyloid fibril

SupramoleculeName: Hemoglobin amyloid fibril / 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: 4.782 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.5912 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 31408
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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