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- EMDB-62440: CRP-HCAb1 complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62440
TitleCRP-HCAb1 complex
Map dataCRPmix1-map
Sample
  • Complex: Pentamer complex of CRP antigen and antibody1
    • Protein or peptide: C-reactive protein
    • Protein or peptide: CRP specific recognition heavy chain antibodie 1 (HCAb1)
KeywordsCRP antigen / Antigen-Antibody complex / 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) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi YJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CRP-HCAb1 complex
Authors: Li YJ
History
DepositionNov 16, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62440.png

Downloads & links

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Map

FileDownload / File: emd_62440.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCRPmix1-map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-0.38888514 - 0.6843268
Average (Standard dev.)-0.000031132487 (±0.028514098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62440_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_62440_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 : Pentamer complex of CRP antigen and antibody1

EntireName: Pentamer complex of CRP antigen and antibody1
Components
  • Complex: Pentamer complex of CRP antigen and antibody1
    • Protein or peptide: C-reactive protein
    • Protein or peptide: CRP specific recognition heavy chain antibodie 1 (HCAb1)

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Supramolecule #1: Pentamer complex of CRP antigen and antibody1

SupramoleculeName: Pentamer complex of CRP antigen and antibody1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 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: CRP specific recognition heavy chain antibodie 1 (HCAb1)

MacromoleculeName: CRP specific recognition heavy chain antibodie 1 (HCAb1)
type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 12.682225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADVQLVESG GGLVQAGESL RLSCTASINI AGLAMGWYRQ APGKQRELAA LSTNSGTTIY GNSVKGRFTI SRDNAKKTVY LQVDSLKPE DTGIYYCNVR FNPDRIYWGQ GTQVTVSS

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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 / Details: 20mM Tris-HCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 481080
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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