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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 / opsonization / complement component C1q complex binding / 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 / opsonization / complement component C1q complex binding / 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 space / 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: To Be Published
Title: Cryo-EM structure of the human CRP-CPS23F complex
Authors: Chen DY / Xie YF / Gao F / Qi JX / Zhang JR
History
DepositionMar 19, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing 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

Projections

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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