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- PDB-3d5r: Crystal Structure of Efb-C (N138A) / C3d Complex -

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Basic information

Entry
Database: PDB / ID: 3d5r
TitleCrystal Structure of Efb-C (N138A) / C3d Complex
Components
  • Complement C3
  • Fibrinogen-binding protein
KeywordsCELL ADHESION/TOXIN / Protein-protein complex / cell adhesion-toxin complex / site-directed mutation / Age-related macular degeneration / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Disease mutation / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Polymorphism / Secreted / Thioester bond
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / 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 / Alternative complement activation / Activation of C3 and C5 ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / 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 / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / 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 / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of protein phosphorylation / G alpha (i) signalling events / secretory granule lumen / blood microparticle / 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
Extracellular fibrinogen binding protein, C-terminal / Efb, C-terminal domain superfamily / Extracellular fibrinogen binding protein C terminal / Sbi, C3 binding domain IV / Sbi, C3 binding domain IV / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment ...Extracellular fibrinogen binding protein, C-terminal / Efb, C-terminal domain superfamily / Extracellular fibrinogen binding protein C terminal / Sbi, C3 binding domain IV / Sbi, C3 binding domain IV / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Arc Repressor Mutant, subunit A / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fibrinogen-binding protein / Complement C3
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus str. Newman (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGeisbrecht, B.V.
CitationJournal: Protein Sci. / Year: 2008
Title: Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.
Authors: Haspel, N. / Ricklin, D. / Geisbrecht, B.V. / Kavraki, L.E. / Lambris, J.D.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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: Fibrinogen-binding protein
B: Complement C3
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)81,3884
Polymers81,3884
Non-polymers00
Water2,702150
1
A: Complement C3
C: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)40,6942
Polymers40,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C3
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)40,6942
Polymers40,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.010, 91.010, 120.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 33143.879 Da / Num. of mol.: 2 / Fragment: Complement C3d fragment, UNP residues 996-1287 / Mutation: C1010A
Source method: isolated from a genetically manipulated source
Details: C3d coding sequence contains site-directed C1010A mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01024
#2: Protein Fibrinogen-binding protein


Mass: 7549.876 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 101-165 / Mutation: N138A
Source method: isolated from a genetically manipulated source
Details: Efb-C coding seqeuence contains N138A site-directed mutation
Source: (gene. exp.) Staphylococcus aureus subsp. aureus str. Newman (bacteria)
Strain: Mu50 / Gene: fib, efb, fib, efb, NWMN_1069 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QG59
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% (v/v) tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 56794 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.103 / Χ2: 0.993 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.415 / Num. unique all: 5503 / Χ2: 0.828 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.41 / Cor.coef. Fo:Fc: 0.668
Highest resolutionLowest resolution
Rotation2.1 Å27.99 Å
Translation2.1 Å27.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GOX

2gox


Resolution: 2.1→50 Å / FOM work R set: 0.826 / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.241 2727 random
Rwork0.218 --
obs-53911 -
Displacement parametersBiso mean: 41.053 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 0 150 5868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006256
X-RAY DIFFRACTIONc_angle_deg1.17423

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