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- EMDB-13470: C-reactive protein decamer at pH 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-13470
TitleC-reactive protein decamer at pH 5
Map data
Sample
  • Complex: C-reactive protein decamer
    • Protein or peptide: C-reactive protein
  • Ligand: CALCIUM ION
  • Ligand: water
Function / homology
Function and homology information


regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / 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: 2.8 Å
AuthorsNoone DP / Sharp TH
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)759517European Union
CitationJournal: Front Immunol / Year: 2021
Title: Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such as Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein.
Authors: Dylan P Noone / Tijn T van der Velden / Thomas H Sharp /
Abstract: The pentraxin family of proteins includes C-reactive protein (CRP), a canonical marker for the acute phase inflammatory response. As compared to normal physiological conditions in human serum, under ...The pentraxin family of proteins includes C-reactive protein (CRP), a canonical marker for the acute phase inflammatory response. As compared to normal physiological conditions in human serum, under conditions associated with damage and inflammation, such as acidosis and the oxidative burst, CRP exhibits modulated biochemical properties that may have a structural basis. Here, we explore how pH and ligand binding affect the structure and biochemical properties of CRP. Cryo-electron microscopy was used to solve structures of CRP at pH 7.5 or pH 5 and in the presence or absence of the ligand phosphocholine (PCh), which yielded 7 new high-resolution structures of CRP, including pentameric and decameric complexes. Structures previously derived from crystallography were imperfect pentagons, as shown by the variable angles between each subunit, whereas pentameric CRP derived from cryoEM was found to have C5 symmetry, with subunits forming a regular pentagon with equal angles. This discrepancy indicates flexibility at the interfaces of monomers that may relate to activation of the complement system by the C1 complex. CRP also appears to readily decamerise in solution into dimers of pentamers, which obscures the postulated binding sites for C1. Subtle structural rearrangements were observed between the conditions tested, including a putative change in histidine protonation that may prime the disulphide bridges for reduction and enhanced ability to activate the immune system. Enzyme-linked immunosorbent assays showed that CRP had markedly increased association to the C1 complex and immunoglobulins under conditions associated with acidosis, whilst a reduction in the Ca concentration lowered this pH-sensitivity for C1q, but not immunoglobulins, suggesting different modes of binding. These data suggest a model whereby a change in the ionic nature of CRP and immunological proteins can make it more adhesive to potential ligands without large structural rearrangements.
History
DepositionAug 25, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateJan 12, 2022-
Current statusJan 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pkf
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13470.png

Downloads & links

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Map

FileDownload / File: emd_13470.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0171 / Movie #1: 0.0171
Minimum - Maximum-0.056922626 - 0.11134526
Average (Standard dev.)8.669275e-05 (±0.002381741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8360.8360.836
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z300.960300.960300.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0570.1110.000

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Supplemental data

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Mask #1

Fileemd_13470_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13470_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13470_half_map_2.map
Projections & Slices
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Sample components

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Entire : C-reactive protein decamer

EntireName: C-reactive protein decamer
Components
  • Complex: C-reactive protein decamer
    • Protein or peptide: C-reactive protein
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: C-reactive protein decamer

SupramoleculeName: C-reactive protein decamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: C-reactive protein

MacromoleculeName: C-reactive protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.068039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 20 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration6 mg/mL
BufferpH: 5
Component:
ConcentrationNameFormula
140.0 mMSodium Acetate
Acetic Acid
140.0 mMNaCl
2.0 mMCaCl2
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 65 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Gatan BioQuantum K3
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3131 / Average exposure time: 2.25 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 740919
CTF correctionSoftware - Name: RELION (ver. 3.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1b09

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 362064
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1b09

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7pkf:
C-reactive protein decamer at pH 5

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