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- EMDB-62138: Pentraxin Domain of PTX3 Dimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62138
TitlePentraxin Domain of PTX3 Dimer
Map data
Sample
  • Cell: Pentraxin Domain of PTX3 Dimer
    • Protein or peptide: Pentraxin-related protein PTX3
Keywordsdimer / immune system
Function / homology
Function and homology information


(1->3)-beta-D-glucan binding / negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / host-mediated suppression of viral proces / opsonization / complement component C1q complex binding / response to yeast / host-mediated suppression of symbiont invasion / virion binding ...(1->3)-beta-D-glucan binding / negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / host-mediated suppression of viral proces / opsonization / complement component C1q complex binding / response to yeast / host-mediated suppression of symbiont invasion / virion binding / extracellular matrix organization / extracellular matrix / positive regulation of phagocytosis / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / inflammatory response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Pentraxin-related protein PTX3 / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Pentraxin-related protein PTX3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsGuo HH / Zhang HW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Pentraxin Domain of PTX3 Dimer
Authors: Guo HH / Zhang HW
History
DepositionOct 22, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62138.png

Downloads & links

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Map

FileDownload / File: emd_62138.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6235936 - 0.8397916
Average (Standard dev.)-0.0001474306 (±0.04398182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 256.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62138_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62138_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 : Pentraxin Domain of PTX3 Dimer

EntireName: Pentraxin Domain of PTX3 Dimer
Components
  • Cell: Pentraxin Domain of PTX3 Dimer
    • Protein or peptide: Pentraxin-related protein PTX3

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Supramolecule #1: Pentraxin Domain of PTX3 Dimer

SupramoleculeName: Pentraxin Domain of PTX3 Dimer / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pentraxin-related protein PTX3

MacromoleculeName: Pentraxin-related protein PTX3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.520561 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: LPAGCETAIL FPMRSKKIFG SVHPVRPMRL ESFSACIWVK ATDVLNKTIL FSYGTKRNPY EIQLYLSYQS IVFVVGGEEN KLVAEAMVS LGRWTHLCGT WNSEEGLTSL WVNGELAATT VEMATGHIVP EGGILQIGQE KNGCCVGGGF DETLAFSGRL T GFNIWDSV ...String:
LPAGCETAIL FPMRSKKIFG SVHPVRPMRL ESFSACIWVK ATDVLNKTIL FSYGTKRNPY EIQLYLSYQS IVFVVGGEEN KLVAEAMVS LGRWTHLCGT WNSEEGLTSL WVNGELAATT VEMATGHIVP EGGILQIGQE KNGCCVGGGF DETLAFSGRL T GFNIWDSV LSNEEIRETG GAESCHIRGN IVGWGVTEIQ PHGGAQYVS

UniProtKB: Pentraxin-related protein PTX3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: OTHER / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zl1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65853
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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