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- PDB-9u4e: Cryo-EM structure of the human CRP-CPS23F complex -

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Basic information

Entry
Database: PDB / ID: 9u4e
TitleCryo-EM structure of the human CRP-CPS23F complex
ComponentsC-reactive protein
KeywordsIMMUNE SYSTEM / complex / pentamer / anti-bacterial immunity
Function / homology
Function and homology information


regulation of interleukin-8 production / complement component C1q complex binding / opsonization / low-density lipoprotein particle binding / vasoconstriction / choline binding / negative regulation of mononuclear cell proliferation / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / complement component C1q complex binding / opsonization / low-density lipoprotein particle binding / vasoconstriction / choline binding / negative regulation of mononuclear cell proliferation / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of superoxide anion generation / acute-phase response / defense response to Gram-positive bacterium / inflammatory response / innate immune response / calcium ion binding / positive regulation of gene expression / : / extracellular region / identical protein binding
Similarity search - Function
: / 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
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsChen, D.Y. / Xie, Y.F. / Gao, F. / Qi, J.X. / Zhang, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2025
Title: C-reactive protein is a broad-spectrum capsule-binding receptor for hepatic capture of blood-borne bacteria.
Authors: Danyu Chen / Jiao Hu / Mengran Zhu / Yufeng Xie / Hantian Yao / Haoran An / Yumin Meng / Juanjuan Wang / Xueting Huang / Yanni Liu / Zhujun Shao / Ye Xiang / Jianxun Qi / George Fu Gao / Jing-Ren Zhang /
Abstract: Plasma C-reactive protein (CRP) is widely used as a biomarker for bacterial infections due to its massive induction during infections. However, the biological function of CRP remains largely ...Plasma C-reactive protein (CRP) is widely used as a biomarker for bacterial infections due to its massive induction during infections. However, the biological function of CRP remains largely undefined. Here we show that CRP enables liver resident macrophages (Kupffer cells) to capture and eliminate a wide range of invasive bacteria from the bloodstream of mice, and thereby provides rapid and sterilizing immunity. Mechanistically, CRP binds to at least 20 capsule types of Gram-positive and -negative pathogens, and shuffles the encapsulated bacteria to Kupffer cells embedded in the lining of the liver sinusoidal vasculatures by the complement-dependent and -independent pathways. The complement-dependent mode involves the activation of complement C3 at the bacterial surface, and the capture of the C3-opsonized bacteria by the CRIg and CR3 complement receptors on Kupffer cells. Cryo-electron microscopy analysis revealed a flexible structural framework for CRP's recognition of structurally diverse capsular polysaccharides. Because human CRP also possesses the broad capsule-binding activities, our findings provide a biological reason for the massive rise of plasma CRP during bacterial infections.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-reactive protein
B: C-reactive protein
C: C-reactive protein
D: C-reactive protein
E: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,65120
Polymers125,3075
Non-polymers4,34415
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
C-reactive protein


Mass: 25061.477 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRP, PTX1 / Production host: Homo sapiens (human) / References: UniProt: P02741
#2: Polysaccharide
alpha-L-rhamnopyranose-(1-2)-1,3-bis(oxidanyl)propan-2-yl [(2~{R},3~{S},4~{S},5~{R})-2- ...alpha-L-rhamnopyranose-(1-2)-1,3-bis(oxidanyl)propan-2-yl [(2~{R},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-3,5,6-tris(oxidanyl)oxan-4-yl] hydrogen phosphate-(1-4)-beta-L-rhamnopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 788.636 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
[][b-D-Glcp]{[(4+1)][b-L-Rhap]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Rhap]{}[(3+0)][P]{[(0+1)][<C3O2>]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of C-reactive protein and CPS23F / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207101 / Symmetry type: POINT
RefinementHighest resolution: 2.78 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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