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- EMDB-2403: Structure of Human C3bBb convertase bound to a fragment of Properdin -

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Entry
Database: EMDB / ID: EMD-2403
TitleStructure of Human C3bBb convertase bound to a fragment of Properdin
Map dataStructure of Human C3bBb convertase bound to a fragment of Properdin
Sample
  • Sample: Structure of Human C3bBb convertase bound to a fragment of Properdin
  • Protein or peptide: Fragment Bb from Complement factor B
  • Protein or peptide: Fragment C3b from Complement component C3
  • Protein or peptide: Complement Factor P
Keywordsproperdin / C3b / AP C3 convertase / complement / electron microscopy / EM
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / complement binding ...cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / regulation of complement activation / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / negative regulation of endopeptidase activity / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / positive regulation of phagocytosis / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / specific granule lumen / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of immune response / tertiary granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / defense response to bacterium / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Thrombospondin type 1 repeat / Complement factor B / Complement B/C2 / Complement B/C2 / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 ...: / : / Thrombospondin type 1 repeat / Complement factor B / Complement B/C2 / Complement B/C2 / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Thrombospondin type-1 (TSP1) repeat / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan / Peptidase S1, PA clan / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement factor B / Complement C3 / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 29.3 Å
AuthorsAlcorlo M / Tortajada A / Rodriguez de Cordoba S / Llorca O
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Structural basis for the stabilization of the complement alternative pathway C3 convertase by properdin.
Authors: Martín Alcorlo / Agustín Tortajada / Santiago Rodríguez de Córdoba / Oscar Llorca /
Abstract: Complement is an essential component of innate immunity. Its activation results in the assembly of unstable protease complexes, denominated C3/C5 convertases, leading to inflammation and lysis. ...Complement is an essential component of innate immunity. Its activation results in the assembly of unstable protease complexes, denominated C3/C5 convertases, leading to inflammation and lysis. Regulatory proteins inactivate C3/C5 convertases on host surfaces to avoid collateral tissue damage. On pathogen surfaces, properdin stabilizes C3/C5 convertases to efficiently fight infection. How properdin performs this function is, however, unclear. Using electron microscopy we show that the N- and C-terminal ends of adjacent monomers in properdin oligomers conform a curly vertex that holds together the AP convertase, interacting with both the C345C and vWA domains of C3b and Bb, respectively. Properdin also promotes a large displacement of the TED (thioester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domains of C3b, which likely impairs C3-convertase inactivation by regulatory proteins. The combined effect of molecular cross-linking and structural reorganization increases stability of the C3 convertase and facilitates recruitment of fluid-phase C3 convertase to the cell surfaces. Our model explains how properdin mediates the assembly of stabilized C3/C5-convertase clusters, which helps to localize complement amplification to pathogen surfaces.
History
DepositionJun 25, 2013-
Header (metadata) releaseJul 24, 2013-
Map releaseJul 24, 2013-
UpdateApr 15, 2015-
Current statusApr 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11.9
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2403.jpg

Downloads & links

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Map

FileDownload / File: emd_2403.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Human C3bBb convertase bound to a fragment of Properdin
Voxel sizeX=Y=Z: 5.68 Å
Density
Contour LevelBy AUTHOR: 11.9 / Movie #1: 11.9
Minimum - Maximum-29.33714294 - 87.169342040000004
Average (Standard dev.)-0.08180776 (±3.83269167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-30-30
Dimensions606060
Spacing606060
CellA=B=C: 340.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.685.685.68
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z340.800340.800340.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-29.33787.169-0.082

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Supplemental data

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Sample components

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Entire : Structure of Human C3bBb convertase bound to a fragment of Properdin

EntireName: Structure of Human C3bBb convertase bound to a fragment of Properdin
Components
  • Sample: Structure of Human C3bBb convertase bound to a fragment of Properdin
  • Protein or peptide: Fragment Bb from Complement factor B
  • Protein or peptide: Fragment C3b from Complement component C3
  • Protein or peptide: Complement Factor P

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Supramolecule #1000: Structure of Human C3bBb convertase bound to a fragment of Properdin

SupramoleculeName: Structure of Human C3bBb convertase bound to a fragment of Properdin
type: sample / ID: 1000
Details: The structure corresponds to Human C3bBb convertase bound to a Properdin vertex
Number unique components: 3
Molecular weightTheoretical: 285 KDa

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Macromolecule #1: Fragment Bb from Complement factor B

MacromoleculeName: Fragment Bb from Complement factor B / type: protein_or_peptide / ID: 1 / Name.synonym: Bb / Details: Fragment Bb from factor B / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: plasma
Molecular weightTheoretical: 60 KDa
SequenceUniProtKB: Complement factor B
GO: extracellular region, plasma membrane, complement binding, serine-type endopeptidase activity, complement activation, alternative pathway, proteolysis, regulation of complement activation
InterPro: Complement B/C2, Serine proteases, trypsin domain, Serine proteases, trypsin family, histidine active site, Peptidase S1A, chymotrypsin family, Sushi/SCR/CCP domain, Peptidase S1, PA clan, ...InterPro: Complement B/C2, Serine proteases, trypsin domain, Serine proteases, trypsin family, histidine active site, Peptidase S1A, chymotrypsin family, Sushi/SCR/CCP domain, Peptidase S1, PA clan, von Willebrand factor, type A

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Macromolecule #2: Fragment C3b from Complement component C3

MacromoleculeName: Fragment C3b from Complement component C3 / type: protein_or_peptide / ID: 2 / Name.synonym: C3b / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: plasma
Molecular weightTheoretical: 180 KDa
SequenceUniProtKB: Complement C3
GO: extracellular space, extracellular exosome, plasma membrane, C5L2 anaphylatoxin chemotactic receptor binding, endopeptidase inhibitor activity, complement activation, alternative pathway, ...GO: extracellular space, extracellular exosome, plasma membrane, C5L2 anaphylatoxin chemotactic receptor binding, endopeptidase inhibitor activity, complement activation, alternative pathway, complement activation, classical pathway, fatty acid metabolic process, G protein-coupled receptor signaling pathway, inflammatory response, negative regulation of endopeptidase activity, positive regulation of activation of membrane attack complex, positive regulation of angiogenesis, positive regulation of G protein-coupled receptor signaling pathway, positive regulation of glucose transmembrane transport, positive regulation of lipid storage, positive regulation of phagocytosis, positive regulation of protein phosphorylation, positive regulation of type IIa hypersensitivity, positive regulation of vascular endothelial growth factor production, regulation of complement activation, regulation of triglyceride biosynthetic process
InterPro: Alpha-macroglobulin, receptor-binding, Alpha-macroglobulin-like, TED domain, Macroglobulin domain, Alpha-2-macroglobulin, bait region domain, Anaphylatoxin/fibulin, Anaphylatoxin, ...InterPro: Alpha-macroglobulin, receptor-binding, Alpha-macroglobulin-like, TED domain, Macroglobulin domain, Alpha-2-macroglobulin, bait region domain, Anaphylatoxin/fibulin, Anaphylatoxin, complement system, Anaphylatoxin, complement system domain, Alpha-2-macroglobulin, Alpha-2-macroglobulin, conserved site, INTERPRO: IPR019565, Netrin domain, Netrin module, non-TIMP type, Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid, Tissue inhibitor of metalloproteinases-like, OB-fold

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Macromolecule #3: Complement Factor P

MacromoleculeName: Complement Factor P / type: protein_or_peptide / ID: 3 / Name.synonym: Properdin / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: plasma
Molecular weightTheoretical: 30 KDa
SequenceUniProtKB: Properdin
GO: extracellular space, complement activation, alternative pathway, defense response to bacterium, regulation of complement activation
InterPro: Thrombospondin type-1 (TSP1) repeat

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: 20 mM Hepes, 75 mM NaCl and 5 mM MgCl2
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1% w/v uranyl acetate for 15 seconds
GridDetails: 400 mesh copper carbon only (50ct), glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 54926 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.9 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL / Tilt angle max: 40
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected using a CMOS camera and the power spectrum
DetailsMicrographs were recorded using a low-dose protocol under control of the EM-TOOLS software (TVIPS)
DateJul 17, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 2.84 µm / Number real images: 1024 / Average electron dose: 10 e/Å2
Details: Micrographs were recorded using a low-dose protocol under control of the EM-TOOLS software (TVIPS) and 4 k x 4 k TVIPS CMOS detector (TemCam-F416)
Bits/pixel: 16
Tilt angle min0

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Image processing

CTF correctionDetails: Each frame, estimated with CTFFIND and corrected using BSOFT
Final two d classificationNumber classes: 128
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 29.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1, EMAN2, Xmipp-2.4 / Number images used: 12324
DetailsThe particles were manually selected using Boxer (EMAN1). Images were classified and averaged using maximum-likelihood multi-reference methods as implemented in XMIPP. Ab initio templates for angular refinement were obtained using the random conical tilt (RCT) method performed using XMIPP. 3D reconstructions were obtained using angular refinement as implemented in EMAN.

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Atomic model buiding 1

Initial modelPDB ID:

2win


Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: J / Chain - #2 - Chain ID: G
SoftwareName: UCSF Chimera
DetailsThe domains were separately fitted using UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation

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