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- PDB-9n20: Structure of C3d Bound to a Fragment of FHR-2 and S. aureus Efb-C -

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Basic information

Entry
Database: PDB / ID: 9n20
TitleStructure of C3d Bound to a Fragment of FHR-2 and S. aureus Efb-C
Components
  • Complement C3dg fragment
  • Complement factor H-related protein 2
  • Fibrinogen-binding protein
KeywordsIMMUNE SYSTEM / complement system / C3 / RCA / inhibitor
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 / complement component C3b binding / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation ...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 / complement component C3b binding / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / complement receptor mediated signaling pathway / positive regulation of D-glucose transmembrane transport / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / : / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / negative regulation of protein binding / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / 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 protein phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding / 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 / : / 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 / : / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / 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 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Complement factor H-related protein 2 / Fibrinogen-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDuan, H. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J Immunol. / Year: 2025
Title: The C-terminal domain of Staphylococcus aureus Efb recruits FHR-2 to C3b, synergistically inhibiting the terminal complement pathway.
Authors: Duan, H. / Kortvely, E. / Mary, J.L. / Hauck, S.M. / Geisbrecht, B.V.
History
DepositionJan 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3dg fragment
C: Fibrinogen-binding protein
B: Complement factor H-related protein 2


Theoretical massNumber of molelcules
Total (without water)56,4033
Polymers56,4033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.584, 145.584, 76.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Complement C3dg fragment


Mass: 33143.879 Da / Num. of mol.: 1 / Fragment: residues 996-1287
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 Fibrinogen-binding protein


Mass: 8597.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: fib, efb, SAV1158 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68799
#3: Protein Complement factor H-related protein 2 / FHR-2 / DDESK59 / H factor-like 3 / H factor-like protein 2


Mass: 14662.505 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFHR2, CFHL2, FHR2, HFL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36980
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: 4.17 Å3/Da / Density % sol: 70.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M imidazole [pH 6.7] 12% (w/v) peg-20k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 14125 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.048 / Rrim(I) all: 0.22 / Χ2: 0.976 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.3-3.4210.71.55613920.5070.820.4721.6310.87999.6
3.42-3.5516.41.24713980.8070.9450.3111.2870.955100
3.55-3.72210.95413990.8920.9710.2120.9780.995100
3.72-3.9122.40.68914050.9460.9860.1480.7050.96100
3.91-4.1622.90.42914000.980.9950.0910.4391.014100
4.16-4.4823.10.30114080.990.9970.0640.3081.037100
4.48-4.9323.10.214150.9950.9990.0420.2040.956100
4.93-5.64230.20514080.9950.9990.0440.210.945100
5.64-7.122.90.1614320.9960.9990.0340.1630.964100
7.1-5022.20.05414680.99810.0120.0550.998100

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.74 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 1333 10 %
Rwork0.1783 --
obs0.1818 13333 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 0 0 3808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023884
X-RAY DIFFRACTIONf_angle_d0.4575250
X-RAY DIFFRACTIONf_dihedral_angle_d4.239513
X-RAY DIFFRACTIONf_chiral_restr0.035581
X-RAY DIFFRACTIONf_plane_restr0.004675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.420.33951130.29011036X-RAY DIFFRACTION82
3.42-3.560.27781220.25991108X-RAY DIFFRACTION88
3.56-3.720.23881260.21881158X-RAY DIFFRACTION92
3.72-3.910.25271330.20081209X-RAY DIFFRACTION95
3.91-4.160.22061370.17661205X-RAY DIFFRACTION96
4.16-4.480.23581370.16791236X-RAY DIFFRACTION97
4.48-4.930.15461390.15061240X-RAY DIFFRACTION98
4.93-5.640.21191400.18091237X-RAY DIFFRACTION98
5.64-7.110.25251420.20211265X-RAY DIFFRACTION98
7.11-48.740.16081440.13391306X-RAY DIFFRACTION99
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)
18.9958-6.2263-4.81554.35683.63827.7220.7519-1.1794-0.6728-0.3105-0.5186-0.09681.04940.4017-0.23961.3286-0.22840.01140.9303-0.10131.057258.2387-65.0287-18.6884
26.16244.44990.63787.93220.98414.0068-0.41860.37360.9086-1.11540.35650.4046-1.1987-0.25630.13371.09450.12890.02860.48710.0370.676765.0601-13.1059-22.5967
36.07550.36770.72934.8558-0.66185.45290.0715-0.3096-0.1371-0.4096-0.0808-0.4277-0.12190.22660.00540.6894-0.11750.11540.438-0.07690.602972.7789-28.7511-15.8209
47.62534.6631-3.15667.1291-2.5136.93651.3931-1.69641.03862.0641-1.13421.2474-0.576-0.6054-0.16811.5783-0.02350.21831.2527-0.26491.209353.9871-5.9382-0.9347
50.259-0.4611-1.14074.8760.48265.6322-0.3932-1.04361.6630.2925-0.45590.662-0.8222-0.58840.08761.41710.31670.04940.7294-0.34181.290662.3068-4.8334-8.2626
65.66194.96432.87154.69873.91567.3655-1.28880.0370.8891-0.27840.77471.2825-1.7105-1.1830.89781.53010.3938-0.18491.0133-0.01411.490956.19940.7023-11.506
73.2626-3.5107-3.34243.90873.88414.0394-0.04370.00210.01240.936-0.37411.3248-0.999-1.21920.37920.9170.25420.23041.52670.03211.404139.7127-26.6695-6.1543
84.65710.7736-3.25962.5462-0.15552.53551.66840.14190.5284-0.9811-0.82351.6674-1.8424-2.5148-0.29151.22590.63640.07991.5959-0.03021.978237.6532-20.5708-10.4067
92.7385-2.9677-4.24436.20534.51189.3987-0.06510.7757-0.03550.4038-0.15651.5226-0.252-2.42870.29050.7532-0.2082-0.02691.5509-0.06451.588340.6839-36.0837-12.4681
106.1767-5.72376.29435.3114-5.83026.42520.1451-0.53481.4165-2.2082-0.0354-1.07841.08370.3360.10061.433-0.23080.18391.2471-0.18870.831761.8099-57.6603-20.2167
116.4534-6.71140.16227.55580.12227.72930.69322.3815-0.4008-2.3438-1.4190.32140.5285-0.0510.5621.2719-0.447-0.05551.215-0.06141.132854.4845-55.8929-25.1112
125.59287.00624.05348.98755.23793.05910.3575-1.15812.8878-1.40691.03882.37940.50590.4807-1.37982.6131-0.12650.32750.9038-0.06891.793553.0807-68.9587-18.0902
138.1835-3.1079-2.48721.22480.90417.82140.2123-0.0538-1.2210.02070.01540.55830.8516-1.5795-0.08061.0665-0.61440.01391.278-0.09611.086547.1575-55.9869-17.6498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 262 through 270 )
2X-RAY DIFFRACTION2chain 'A' and (resid 994 through 1110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1111 through 1287 )
4X-RAY DIFFRACTION4chain 'C' and (resid 101 through 123 )
5X-RAY DIFFRACTION5chain 'C' and (resid 124 through 141 )
6X-RAY DIFFRACTION6chain 'C' and (resid 142 through 165 )
7X-RAY DIFFRACTION7chain 'B' and (resid 146 through 160 )
8X-RAY DIFFRACTION8chain 'B' and (resid 161 through 175 )
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 210 )
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 221 )
11X-RAY DIFFRACTION11chain 'B' and (resid 222 through 246 )
12X-RAY DIFFRACTION12chain 'B' and (resid 247 through 251 )
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 261 )

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