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- EMDB-63844: Cryo-EM structure of the human CRP-CPS23F complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63844
TitleCryo-EM structure of the human CRP-CPS23F complex
Map data
Sample
  • Complex: Complex of C-reactive protein and CPS23F
    • Protein or peptide: C-reactive protein
  • Ligand: CALCIUM ION
Keywordscomplex / pentamer / anti-bacterial immunity / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsChen DY / Xie YF / Gao F / Qi JX / Zhang JR
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63844.png

Downloads & links

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Map

FileDownload / File: emd_63844.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.0017852748 - 1.7165937
Average (Standard dev.)0.0010414713 (±0.024764396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63844_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_63844_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of C-reactive protein and CPS23F

EntireName: Complex of C-reactive protein and CPS23F
Components
  • Complex: Complex of C-reactive protein and CPS23F
    • Protein or peptide: C-reactive protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Complex of C-reactive protein and CPS23F

SupramoleculeName: Complex of C-reactive protein and CPS23F / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-reactive protein

MacromoleculeName: C-reactive protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.061477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKLLCFLVL TSLSHAFGQT DMSRKAFVFP KESDTSYVSL KAPLTKPLKA FTVCLHFYTE LSSTRGYSIF SYATKRQDNE ILIFWSKDI GYSFTVGGSE ILFEVPEVTV APVHICTSWE SASGIVEFWV DGKPRVRKSL KKGYTVGAEA SIILGQEQDS F GGNFEGSQ ...String:
MEKLLCFLVL TSLSHAFGQT DMSRKAFVFP KESDTSYVSL KAPLTKPLKA FTVCLHFYTE LSSTRGYSIF SYATKRQDNE ILIFWSKDI GYSFTVGGSE ILFEVPEVTV APVHICTSWE SASGIVEFWV DGKPRVRKSL KKGYTVGAEA SIILGQEQDS F GGNFEGSQ SLVGDIGNVN MWDFVLSPDE INTIYLGGPF SPNVLNWRAL KYEVQGEVFT KPQLWP

UniProtKB: C-reactive protein

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1b09

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207101
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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