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- PDB-9k6u: Pentraxin Domain of PTX3 Octamer -

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Basic information

Entry
Database: PDB / ID: 9k6u
TitlePentraxin Domain of PTX3 Octamer
ComponentsPentraxin-related protein PTX3
KeywordsIMMUNE SYSTEM / octamer
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGuo, H.H. / Zhang, H.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Pentraxin Domain of PTX3 Octamer
Authors: Guo, H.H. / Zhang, H.W.
History
DepositionOct 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Pentraxin-related protein PTX3
A: Pentraxin-related protein PTX3
D: Pentraxin-related protein PTX3
C: Pentraxin-related protein PTX3
E: Pentraxin-related protein PTX3
H: Pentraxin-related protein PTX3
G: Pentraxin-related protein PTX3
F: Pentraxin-related protein PTX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,42416
Polymers181,6548
Non-polymers1,7708
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pentraxin-related protein PTX3 / Pentaxin-related protein PTX3 / Tumor necrosis factor alpha-induced protein 5 / TNF alpha-induced ...Pentaxin-related protein PTX3 / Tumor necrosis factor alpha-induced protein 5 / TNF alpha-induced protein 5 / Tumor necrosis factor-inducible gene 14 protein / TSG-14


Mass: 22706.770 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTX3, TNFAIP5, TSG14 / Cell (production host): 293F / Production host: Mammalia (mammals) / References: UniProt: P26022
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentraxin Domain of PTX3 Octamer / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalia (mammals) / Cell: 293F
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: OTHER

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121916 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413176
ELECTRON MICROSCOPYf_angle_d0.54117888
ELECTRON MICROSCOPYf_dihedral_angle_d6.2241808
ELECTRON MICROSCOPYf_chiral_restr0.0481992
ELECTRON MICROSCOPYf_plane_restr0.0032272

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