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- EMDB-64950: Binding site between C-reactive protein and c2cc monoclonal antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-64950
TitleBinding site between C-reactive protein and c2cc monoclonal antibody
Map data
Sample
  • Complex: Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodies
    • Complex: Human C-reactive protein
      • Protein or peptide: C-reactive protein
    • Complex: Monoclonal antibody
      • Protein or peptide: Monoclonal IgG antibody heavy chain fragment
      • Protein or peptide: Monoclonal IgG antibody light chain fragment
Keywordsc-reactive protein / CRP / monoclonal antibody / immune complex / IgG / 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) / Mus musculus albula (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMoiseenko AV / Kalikin AV
Funding support1 items
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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64950.png

Downloads & links

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Map

FileDownload / File: emd_64950.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 450 pix.
= 373.5 Å		0.83 Å/pix.
x 450 pix.
= 373.5 Å		0.83 Å/pix.
x 450 pix.
= 373.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.285
Minimum - Maximum-14.553406000000001 - 21.325195000000001
Average (Standard dev.)0.0009921428 (±0.043492828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 373.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64950_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64950_half_map_1.map
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Half map: #1

Fileemd_64950_half_map_2.map
Projections & Slices
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Sample components

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Entire : Asymmetric unit of D5-symmetric complex composed of two pentameri...

EntireName: Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodies
Components
  • Complex: Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodies
    • Complex: Human C-reactive protein
      • Protein or peptide: C-reactive protein
    • Complex: Monoclonal antibody
      • Protein or peptide: Monoclonal IgG antibody heavy chain fragment
      • Protein or peptide: Monoclonal IgG antibody light chain fragment

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Supramolecule #1: Asymmetric unit of D5-symmetric complex composed of two pentameri...

SupramoleculeName: Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Human C-reactive protein

SupramoleculeName: Human C-reactive protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Monoclonal antibody

SupramoleculeName: Monoclonal antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus albula (mammal)

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Macromolecule #1: C-reactive protein

MacromoleculeName: C-reactive protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.068039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTDMSRKAFV FPKESDTSYV SLKAPLTKPL KAFTVCLHFY TELSSTRGYS IFSYATKRQD NEILIFWSKD IGYSFTVGGS EILFEVPEV TVAPVHICTS WESASGIVEF WVDGKPRVRK SLKKGYTVGA EASIILGQEQ DSFGGNFEGS QSLVGDIGNV N MWDFVLSP ...String:
QTDMSRKAFV FPKESDTSYV SLKAPLTKPL KAFTVCLHFY TELSSTRGYS IFSYATKRQD NEILIFWSKD IGYSFTVGGS EILFEVPEV TVAPVHICTS WESASGIVEF WVDGKPRVRK SLKKGYTVGA EASIILGQEQ DSFGGNFEGS QSLVGDIGNV N MWDFVLSP DEINTIYLGG PFSPNVLNWR ALKYEVQGEV FTKPQLWP

UniProtKB: C-reactive protein

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Macromolecule #2: Monoclonal IgG antibody heavy chain fragment

MacromoleculeName: Monoclonal IgG antibody heavy chain fragment / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus albula (mammal)
Molecular weightTheoretical: 49.078094 KDa
Recombinant expressionOrganism: Mus musculus albula (mammal)
SequenceString: QVQLQQSGTE LSKPGTGVKM SCKASGYTFI SYWMHWVKQR PGQGLEWIGY INPSTDSTDY NQNFKDKATM TVDKSSTTAY MQLSTITSE DSAVYFCARS HYLSWDFDVW GAGTTVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String:
QVQLQQSGTE LSKPGTGVKM SCKASGYTFI SYWMHWVKQR PGQGLEWIGY INPSTDSTDY NQNFKDKATM TVDKSSTTAY MQLSTITSE DSAVYFCARS HYLSWDFDVW GAGTTVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP RDCGCKPCIC TVPEVSSVFI FP PKPKDVL TITLTPKVTC VVVDISKDDP EVQFSWFVDD VEVHTAQTQP REEQFNSTFR SVSELPIMHQ DWLNGKEFKC RVN SAAFPA PIEKTISKTK GRPKAPQVYT IPPPKEQMAK DKVSLTCMIT DFFPEDITVE WQWNGQPAEN YKNTQPIMDT DGSY FVYSK LNVQKSNWEA GNTFTCSVLH EGLHNHHTEK SLSHSPGK

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Macromolecule #3: Monoclonal IgG antibody light chain fragment

MacromoleculeName: Monoclonal IgG antibody light chain fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus albula (mammal)
Molecular weightTheoretical: 23.957445 KDa
Recombinant expressionOrganism: Mus musculus albula (mammal)
SequenceString: DIVLTQSPAS LAVSLGQRAT ISCRASQSVS TSGYSYIHWY QQKPGHPPKL LIKYASNLDS GVPARFSGSG SGTDFTLNIH PVEEEDAAT YFCQHSWELP LTFGAGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPAS LAVSLGQRAT ISCRASQSVS TSGYSYIHWY QQKPGHPPKL LIKYASNLDS GVPARFSGSG SGTDFTLNIH PVEEEDAAT YFCQHSWELP LTFGAGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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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

Concentration1 mg/mL
BufferpH: 7.6 / Component:
ConcentrationName
20.0 mMTris-HCl
150.0 mMNaCl

Details: 20 mM Tris-HCl buffer (pH 7.6), containing 150 mM NaCl
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

Particle selectionNumber selected: 286000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6)
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
Number images used: 1434575
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Ab-initio without symmetry
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Details: Local refinement made with the mask covering one chain of pCRP and one Fab fragment. The local refinement was performed with symmetry expanded set of particles, prealigned to a C5-symmetric ...Details: Local refinement made with the mask covering one chain of pCRP and one Fab fragment. The local refinement was performed with symmetry expanded set of particles, prealigned to a C5-symmetric consensus reconstruction of the whole complex.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

3hc3

source_name: PDB, initial_model_type: experimental modelIgG antibody as a reference model for sequence replacement

7pke

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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