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- PDB-7ue9: Structure of anti-C3d Fab(3d8b) in complex with C3d -

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Basic information

Entry
Database: PDB / ID: 7ue9
TitleStructure of anti-C3d Fab(3d8b) in complex with C3d
Components
  • Complement C3dg fragment
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / Fab / C3d
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 phagocytosis, engulfment / Activation of C3 and C5 ...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 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 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 / positive regulation of protein phosphorylation / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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 ...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 / : / 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 / Glycosyltransferase - #20 / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOlland, A.M. / White, A. / Suto, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Front Immunol / Year: 2022
Title: Development and Optimization of Bifunctional Fusion Proteins to Locally Modulate Complement Activation in Diseased Tissue.
Authors: Fahnoe, K.C. / Liu, F. / Morgan, J.G. / Ryan, S.T. / Storek, M. / Stark, E.G. / Taylor, F.R. / Holers, V.M. / Thurman, J.M. / Wawersik, S. / Kalled, S.L. / Violette, S.M.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Nov 12, 2025Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source / Item: _diffrn_source.pdbx_wavelength_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
C: Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,91713
Polymers110,9973
Non-polymers92110
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.372, 62.229, 85.547
Angle α, β, γ (deg.)90.000, 108.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab light chain


Mass: 26545.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: humanized / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab heavy chain


Mass: 49720.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: humanized / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Complement C3dg fragment


Mass: 34729.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01024
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 15% PEG 10,000, 0.1 M bicine pH 7.6

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.75→49.47 Å / Num. obs: 73836 / % possible obs: 99.5 % / Redundancy: 3.71 % / CC1/2: 0.998 / Net I/σ(I): 15.23
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 11680 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONT

4ont


Resolution: 1.75→49.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.212 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 3673 5 %RANDOM
Rwork0.171 ---
obs0.1725 70146 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.18 Å2 / Biso mean: 21.725 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å2-0.22 Å2
2---0.12 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.75→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5741 0 60 500 6301
Biso mean--42.07 29.31 -
Num. residues----744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136021
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155640
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6438188
X-RAY DIFFRACTIONr_angle_other_deg1.491.57713056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15823.285274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6991525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021350
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 238 -
Rwork0.392 4984 -
obs--96.01 %
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)
10.63930.0219-0.43320.2724-0.11371.2381-0.00370.01230.0126-0.0077-0.01090.05960.03150.00960.01450.0106-0.00160.01720.0033-0.0030.0515-17.24415.65531.378
20.92740.27120.33850.4809-0.08570.47560.011-0.0014-0.0776-0.0143-0.055-0.03490.00010.04450.0440.01650.00260.01970.01130.00920.0589-7.8113.69935.239
30.1130.0208-0.11150.1720.06340.673-0.0004-0.00490.0461-0.01320.0028-0.0020.04220.0275-0.00240.01580.01590.01790.0210.01750.039844.31635.141-2.063
40.93660.3217-0.65480.2153-0.03120.85650.0452-0.07210.00120.0055-0.0784-0.0201-0.044-0.00040.03320.07360.05450.01260.1090.08880.138215.6431.47524.902
50.20890.0498-0.13540.0518-0.03970.11320.00110.00410.0423-0.00360.00990.01980.02050.0064-0.0110.01810.00840.01520.02160.0050.028115.95325.69119.388
60.62650.2402-0.45120.1564-0.20671.229-0.0229-0.06390.02810.00090.034-0.00990.09480.0716-0.01110.02230.01860.01830.0618-0.01770.051119.65126.24837.496
70.99550.43340.63590.71440.15281.1847-0.05010.08640.0484-0.07520.11720.0365-0.0385-0.0328-0.06710.0159-0.01090.0120.0270.01440.039611.43932.0217.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L112 - 219
2X-RAY DIFFRACTION2H112 - 214
3X-RAY DIFFRACTION3C0 - 310
4X-RAY DIFFRACTION4C401 - 404
5X-RAY DIFFRACTION4H501 - 503
6X-RAY DIFFRACTION4L301 - 303
7X-RAY DIFFRACTION5C501 - 661
8X-RAY DIFFRACTION5H601 - 775
9X-RAY DIFFRACTION5L401 - 564
10X-RAY DIFFRACTION6H1 - 111
11X-RAY DIFFRACTION7L1 - 111

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