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- PDB-9vca: Binding site between C-reactive protein and c2cc monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 9vca
TitleBinding site between C-reactive protein and c2cc monoclonal antibody
Components
  • C-reactive protein
  • Monoclonal IgG antibody heavy chain fragment
  • Monoclonal IgG antibody light chain fragment
KeywordsIMMUNE SYSTEM / c-reactive protein / CRP / monoclonal antibody / immune complex / IgG
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)
Mus musculus albula (mammal)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMoiseenko, A.V. / Kalikin, A.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: FEBS J / Year: 2025
Title: Cryo-EM structure of pentameric C-reactive protein in complex with monoclonal IgG antibodies.
Authors: Andrey V Moiseenko / Alexander V Kalikin / Philipp S Orekhov / Nadezhda A Byzova / Anatoly V Zherdev / Konstantin V Shaitan / Boris B Dzantiev / Olga S Sokolova /
Abstract: C-reactive protein (CRP) plays a central role in innate immunity and serves as a key biomarker of inflammation. Despite its clinical importance, the structural basis of CRP interactions with ...C-reactive protein (CRP) plays a central role in innate immunity and serves as a key biomarker of inflammation. Despite its clinical importance, the structural basis of CRP interactions with antibodies remains poorly characterized. Using cryo-electron microscopy (cryo-EM), we resolved the structure of immune complexes formed between pentameric CRP and monoclonal immunoglobulin G (IgG) antibodies at up to 2.4 Å resolution. The complexes display a barrel-shaped architecture, with two CRP pentamers bridged by three to five antibodies. We built an atomic model of the CRP-antibody interface, identifying a binding site on the A-face of CRP mediated exclusively by hydrogen bonds, without salt-bridge formation. These findings provide structural insights into CRP-IgG recognition and offer a basis for the rational design of improved antibodies.
History
DepositionJun 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: C-reactive protein
H: Monoclonal IgG antibody heavy chain fragment
L: Monoclonal IgG antibody light chain fragment


Theoretical massNumber of molelcules
Total (without water)96,1043
Polymers96,1043
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein C-reactive protein


Mass: 23068.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRP, PTX1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P02741
#2: Antibody Monoclonal IgG antibody heavy chain fragment


Mass: 49078.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus albula (mammal) / Production host: Mus musculus albula (mammal)
#3: Antibody Monoclonal IgG antibody light chain fragment


Mass: 23957.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus albula (mammal) / Production host: Mus musculus albula (mammal)
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

Component
IDNameTypeEntity IDParent-IDSource
1Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodiesCOMPLEXall0RECOMBINANT
2Human C-reactive proteinCOMPLEX#11RECOMBINANT
3Monoclonal antibodyCOMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Mus musculus albula (mammal)947985
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Mus musculus albula (mammal)947985
Buffer solutionpH: 7.6
Details: 20 mM Tris-HCl buffer (pH 7.6), containing 150 mM NaCl
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HCl1
2150 mMNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimen contains the both interacting compounds, C-reactive protein and monoclonal IgG antibodies in final concentrations 1 mg/mL. To reach immune complexes formation, equal volumes of ...Details: The specimen contains the both interacting compounds, C-reactive protein and monoclonal IgG antibodies in final concentrations 1 mg/mL. To reach immune complexes formation, equal volumes of C-reactive protein and monoclonal IgG antibodies solutions with concentrations of 2 mg/mL each were mixed and incubated for 1 hour at room temperature.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 / Cs: 2.7 mm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6particle selectionTemplate picker based on manually selected subset
4cryoSPARC4.6CTF correctionPatch CTF estimation
7Coot0.9model fittingSequence replacement, rigid body fitting, combining models
9ISOLDE1.8model refinementMDFF optimization
10PHENIX1.2model refinementReal space refinement on ISOLDE model restrained on itself
11cryoSPARC4.6initial Euler assignmentAb-initio without symmetry
12cryoSPARC4.6final Euler assignment
14cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 286000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1434575
Details: The resolution estimated within a soft mask covering one pCRP chain and one Fab fragment. The number of particles provided after the D5 symmetry expansion
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
13HC3

3hc3

3HC3IgG antibody as a reference model for sequence replacement1
27PKE

7pke

7PKE2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613488
ELECTRON MICROSCOPYf_angle_d0.81944745
ELECTRON MICROSCOPYf_chiral_restr0.0535516
ELECTRON MICROSCOPYf_plane_restr0.0071601
ELECTRON MICROSCOPYf_dihedral_angle_d13.26691228

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