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- PDB-6xzu: Complex of C-terminal domain of murine complement C3b with the hC... -

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Basic information

Entry
Database: PDB / ID: 6xzu
TitleComplex of C-terminal domain of murine complement C3b with the hC3Nb3 nanobody
Components
  • Complement C3
  • nanobody hC3Nb1
KeywordsIMMUNE SYSTEM / complex / complement / nanobody / innate immune system
Function / homology
Function and homology information


Alternative complement activation / : / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process ...Alternative complement activation / : / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / G alpha (i) signalling events / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of developmental growth / positive regulation of phagocytosis, engulfment / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / positive regulation of phagocytosis / Neutrophil degranulation / fatty acid metabolic process / complement activation, classical pathway / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / blood coagulation / positive regulation of ERK1 and ERK2 cascade / inflammatory response / positive regulation of protein phosphorylation / lipid binding / cell surface / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Complement C3-like / 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 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin ...Complement C3-like / 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 / Anaphylatoxin, complement system domain / 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 / 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 / Netrin domain / NTR domain profile. / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAndersen, G.R. / Pedersen, H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: J Immunol. / Year: 2020
Title: A Complement C3-Specific Nanobody for Modulation of the Alternative Cascade Identifies the C-Terminal Domain of C3b as Functional in C5 Convertase Activity.
Authors: Pedersen, H. / Jensen, R.K. / Jensen, J.M.B. / Fox, R. / Pedersen, D.V. / Olesen, H.G. / Hansen, A.G. / Christiansen, D. / Mazarakis, S.M.M. / Lojek, N. / Hansen, P. / Gadeberg, T.A.F. / ...Authors: Pedersen, H. / Jensen, R.K. / Jensen, J.M.B. / Fox, R. / Pedersen, D.V. / Olesen, H.G. / Hansen, A.G. / Christiansen, D. / Mazarakis, S.M.M. / Lojek, N. / Hansen, P. / Gadeberg, T.A.F. / Zarantonello, A. / Laursen, N.S. / Mollnes, T.E. / Johnson, M.B. / Stevens, B. / Thiel, S. / Andersen, G.R.
History
DepositionFeb 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nanobody hC3Nb1
B: Complement C3


Theoretical massNumber of molelcules
Total (without water)31,1372
Polymers31,1372
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 78.250, 121.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Antibody nanobody hC3Nb1


Mass: 13959.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Single domain nanobody selected from lama immunization library
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Complement C3 / HSE-MSF


Mass: 17177.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: From murine complement C3b / Source: (gene. exp.) Mus musculus (house mouse) / Gene: C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P01027
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 17.5% PEG 4K, 33 mM NaOAc (pH 4.3), 66 mM NaOAc (pH 5.3), 0.2 M AmSO4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.5→40.2 Å / Num. obs: 55338 / % possible obs: 98.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.07987 / Rpim(I) all: 0.02283 / Rrim(I) all: 0.08319 / Net I/σ(I): 14.45
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.3 % / Num. unique obs: 5404 / CC1/2: 0.502 / % possible all: 97.02

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_3689refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I07

2i07


Resolution: 1.5→40.19 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3293
RfactorNum. reflection% reflection
Rfree0.2 1677 3.03 %
Rwork0.1656 --
obs0.1666 55338 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 0 311 2432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01632158
X-RAY DIFFRACTIONf_angle_d2.09242915
X-RAY DIFFRACTIONf_chiral_restr0.1244318
X-RAY DIFFRACTIONf_plane_restr0.0144376
X-RAY DIFFRACTIONf_dihedral_angle_d15.7634797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.40931280.3974353X-RAY DIFFRACTION96.93
1.54-1.590.33181440.3044394X-RAY DIFFRACTION97.13
1.59-1.650.20561320.23594385X-RAY DIFFRACTION97.33
1.65-1.720.24471460.20244374X-RAY DIFFRACTION97.56
1.72-1.80.22651370.18344424X-RAY DIFFRACTION97.83
1.8-1.890.23721430.17714448X-RAY DIFFRACTION98.14
1.89-2.010.19081410.17494419X-RAY DIFFRACTION98.09
2.01-2.160.23291350.16264489X-RAY DIFFRACTION98.66
2.16-2.380.19241340.15624515X-RAY DIFFRACTION98.73
2.38-2.730.2011440.16144518X-RAY DIFFRACTION99.13
2.73-3.430.22061430.16154574X-RAY DIFFRACTION99.22
3.43-40.190.15951500.14484768X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 26.9114774278 Å / Origin y: 2.02166971999 Å / Origin z: -10.9014499839 Å
111213212223313233
T0.167849008724 Å2-0.0253022616979 Å20.0322404102276 Å2-0.169399282929 Å2-0.0149544329042 Å2--0.174159679147 Å2
L0.759373205031 °2-0.308854170148 °20.910552751292 °2-1.03651109816 °2-0.512812992578 °2--2.0352838089 °2
S-0.0284939468627 Å °0.0109045427398 Å °0.0703269725017 Å °0.00128188073579 Å °0.00824296772444 Å °-0.0488010516004 Å °-0.164495259053 Å °0.149210606282 Å °0.0317154336783 Å °
Refinement TLS groupSelection details: all

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