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- EMDB-66219: Filament structure of human Reg3alpha -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66219
TitleFilament structure of human Reg3alpha
Map data
Sample
  • Complex: Filaments formed by regenerating islet-derived protein 3-alpha
    • Protein or peptide: Regenerating islet-derived protein 3-alpha 15 kDa form
KeywordsC-type lectin domain containing protein / antimicrobial activity / cryo-EM / protein filament / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion / Antimicrobial peptides / positive regulation of wound healing ...positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion / Antimicrobial peptides / positive regulation of wound healing / acute-phase response / hormone activity / response to wounding / response to peptide hormone / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / carbohydrate binding / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Regenerating islet-derived protein 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsCao Q / Han JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Commun Chem / Year: 2026
Title: Structural basis for human RegIIIalpha filament formation
Authors: Cao Q / Han JT
History
DepositionSep 16, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66219.png

Downloads & links

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Map

FileDownload / File: emd_66219.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: 2.5
Minimum - Maximum-18.712911999999999 - 37.875137000000002
Average (Standard dev.)0.000000000002715 (±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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Half map: #1

Fileemd_66219_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_66219_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 : Filaments formed by regenerating islet-derived protein 3-alpha

EntireName: Filaments formed by regenerating islet-derived protein 3-alpha
Components
  • Complex: Filaments formed by regenerating islet-derived protein 3-alpha
    • Protein or peptide: Regenerating islet-derived protein 3-alpha 15 kDa form

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Supramolecule #1: Filaments formed by regenerating islet-derived protein 3-alpha

SupramoleculeName: Filaments formed by regenerating islet-derived protein 3-alpha
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Regenerating islet-derived protein 3-alpha 15 kDa form

MacromoleculeName: Regenerating islet-derived protein 3-alpha 15 kDa form
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.289049 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
IRCPKGSKAY GSHCYALFLS PKSWTDADLA CQKRPSGNLV SVLSGAEGSF VSSLVKSIGN SYSYVWIGLH DPTQGTEPNG EGWEWSSSD VMNYFAWERN PSTISSPGHC ASLSRSTAFL RWKDYNCNVR LPYVCKFTD

UniProtKB: Regenerating islet-derived protein 3-alpha

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
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: 20.47 Å
Applied symmetry - Helical parameters - Δ&Phi: 54.24 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.0.1) / Number images used: 762506
CTF correctionType: NONE
Segment selectionNumber selected: 802654 / Software - Name: cryoSPARC (ver. V4.0.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mth

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9wtd:
Filament structure of human Reg3alpha

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