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- PDB-2gox: Crystal structure of Efb-C / C3d Complex -

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Basic information

Entry
Database: PDB / ID: 2gox
TitleCrystal structure of Efb-C / C3d Complex
Components
  • Complement C3Complement component 3
  • Fibrinogen-binding protein
KeywordsCELL ADHESION/TOXIN / PROTEIN-PROTEIN COMPLEX / CELL ADHESION-TOXIN COMPLEX
Function / homology
Function and homology information


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 / Alternative complement activation / positive regulation of lipid storage ...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 / 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 / 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 / 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) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / 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 component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain ...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 component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / 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 domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Netrin domain / NTR domain profile. / 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 / 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
Complement C3 / Fibrinogen-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHammel, M. / Geisbrecht, B.V.
CitationJournal: Nat.Immunol. / Year: 2007
Title: A structural basis for complement inhibition by Staphylococcus aureus.
Authors: Hammel, M. / Sfyroera, G. / Ricklin, D. / Magotti, P. / Lambris, J.D. / Geisbrecht, B.V.
History
DepositionApr 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
B: Fibrinogen-binding protein
C: Complement C3
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)81,4744
Polymers81,4744
Non-polymers00
Water5,711317
1
A: Complement C3
B: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Complement C3
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.939, 90.939, 122.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein Complement C3 / Complement component 3


Mass: 33143.879 Da / Num. of mol.: 2 / Fragment: Fragment of alpha chain: Residues 996-1287 / Mutation: C1010A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3 / Plasmid: pT7- / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01024
#2: Protein Fibrinogen-binding protein


Mass: 7592.901 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 101-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Species: Staphylococcus aureus / Strain: Mu50 / ATCC 700699 / Gene: efb / Plasmid: pT7HMT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68799
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 60% Tacsimate pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 50259 / Num. obs: 49761 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Rsym value: 0.092 / Χ2: 0.959 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 92.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4664 / Χ2: 0.753 / % possible all: 92.4

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Phasing

Phasing MRRfactor: 0.4 / Cor.coef. Fo:Fc: 0.646
Highest resolutionLowest resolution
Rotation3 Å45.47 Å
Translation3 Å45.47 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3D

1c3d


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.43 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2519 5.1 %RANDOM
Rwork0.181 ---
all0.184 ---
obs-49718 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.528 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.93 Å2
Refine analyzeLuzzati coordinate error obs: 0.298 Å / Luzzati d res low obs: 2 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 0 317 5991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225780
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9597825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30425.058259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.533151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5841527
X-RAY DIFFRACTIONr_chiral_restr0.1290.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024323
X-RAY DIFFRACTIONr_nbd_refined0.2290.23165
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2341
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.28
X-RAY DIFFRACTIONr_mcbond_it1.1641.53733
X-RAY DIFFRACTIONr_mcangle_it1.86725771
X-RAY DIFFRACTIONr_scbond_it2.97832385
X-RAY DIFFRACTIONr_scangle_it4.374.52054
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 152 -
Rwork0.235 3180 -
obs-3332 89.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45440.32370.05791.1803-0.33520.41270.0714-0.0692-0.0063-0.0138-0.0801-0.0786-0.0405-0.05020.0087-0.0101-0.02380.0046-0.06720.01630.00320.192-40.3390.407
21.28290.3198-0.35610.46390.05290.3788-0.0686-0.0163-0.079-0.06890.0663-0.0085-0.0547-0.04270.0023-0.0663-0.02440.0174-0.00950.0055-0.0017-5.112-65.64813.329
38.28041.85020.66571.03560.45281.27150.3709-0.56310.06320.4694-0.3266-0.511-0.1512-0.2083-0.04430.1234-0.1891-0.1484-0.04120.0183-0.029730.379-37.53924.196
41.49841.57361.14776.37360.85231.4692-0.22460.423-0.5442-0.50340.31710.023-0.235-0.1426-0.0925-0.0175-0.16680.02940.1045-0.1349-0.0398-7.928-75.672-10.379
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA991 - 12871 - 297
22CC991 - 12871 - 297
33BB101 - 1651 - 65
44DD101 - 1651 - 65

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