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- PDB-6rmu: Crystal structure of disulphide-linked human C3d dimer in complex... -

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Basic information

Entry
Database: PDB / ID: 6rmu
TitleCrystal structure of disulphide-linked human C3d dimer in complex with Staphylococcus aureus complement subversion protein Sbi-IV
Components
  • Complement C3
  • Immunoglobulin-binding protein Sbi
KeywordsIMMUNE SYSTEM / Complement / innate immunity / domain swap / Staphylococcus aureus
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / positive regulation of D-glucose transmembrane transport / complement-dependent cytotoxicity / complement activation / complement activation, alternative pathway / IgG binding / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / fatty acid metabolic process / 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) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-binding protein Sbi, domain IV / C3 binding domain 4 of IgG-bind protein SBI / Sbi, C3 binding domain IV / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Protein A, Ig-binding domain / B domain ...Immunoglobulin-binding protein Sbi, domain IV / C3 binding domain 4 of IgG-bind protein SBI / Sbi, C3 binding domain IV / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Protein A, Ig-binding domain / B domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Glycosyltransferase - #20 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / 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 family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Immunoglobulin/albumin-binding domain superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Complement C3 / Immunoglobulin-binding protein Sbi
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWahid, A.A. / van den Elsen, J.M.H. / Crennell, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N022165/1 United Kingdom
CitationJournal: Front Immunol / Year: 2022
Title: Staphylococcal Complement Evasion Protein Sbi Stabilises C3d Dimers by Inducing an N-Terminal Helix Swap
Authors: Dunphy, R.W. / Wahid, A.A. / Back, C.R. / Martin, R.L. / Watts, A.G. / Dodson, C.A. / Crennell, S.J. / van den Elsen, J.M.H.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 16, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C3
C: Immunoglobulin-binding protein Sbi
B: Complement C3
D: Immunoglobulin-binding protein Sbi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2656
Polymers88,0974
Non-polymers1682
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-29 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.518, 115.169, 118.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 34778.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01024
#2: Protein Immunoglobulin-binding protein Sbi


Mass: 9269.509 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: sbi, SAV2418 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q931F4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.07
Details: 0.2 M sodium citrate tribasic dihydrate, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→118.93 Å / Num. obs: 40413 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4153 / CC1/2: 0.791 / Rpim(I) all: 0.266 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WY7

2wy7


Resolution: 2.4→82.733 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.2107 2117 5.27 %
Rwork0.156 --
obs0.1589 40185 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→82.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 11 259 6028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125977
X-RAY DIFFRACTIONf_angle_d1.1028086
X-RAY DIFFRACTIONf_dihedral_angle_d14.283671
X-RAY DIFFRACTIONf_chiral_restr0.052892
X-RAY DIFFRACTIONf_plane_restr0.0071056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45590.29461430.20172496X-RAY DIFFRACTION100
2.4559-2.51730.30251410.19772505X-RAY DIFFRACTION100
2.5173-2.58540.26211260.18992504X-RAY DIFFRACTION100
2.5854-2.66150.26331300.19332505X-RAY DIFFRACTION100
2.6615-2.74740.23821420.19052510X-RAY DIFFRACTION100
2.7474-2.84560.25971510.19252494X-RAY DIFFRACTION100
2.8456-2.95950.25661330.19572528X-RAY DIFFRACTION100
2.9595-3.09420.24421540.17792473X-RAY DIFFRACTION100
3.0942-3.25730.24781430.17352546X-RAY DIFFRACTION100
3.2573-3.46140.24181490.16432509X-RAY DIFFRACTION100
3.4614-3.72870.15441160.14892573X-RAY DIFFRACTION100
3.7287-4.10390.19761390.12722570X-RAY DIFFRACTION100
4.1039-4.69770.1491560.10482532X-RAY DIFFRACTION100
4.6977-5.91840.16851600.13032586X-RAY DIFFRACTION100
5.9184-82.78190.18381340.14812737X-RAY DIFFRACTION100

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