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- PDB-1qsj: N-TERMINALLY TRUNCATED C3DG FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1qsj
TitleN-TERMINALLY TRUNCATED C3DG FRAGMENT
ComponentsCOMPLEMENT C3 PRECURSOR
KeywordsIMMUNE SYSTEM / ALPHA-ALPHA BARREL
Function / homology
Function and homology information


Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Peptide ligand-binding receptors / vascular associated smooth muscle cell differentiation / C5L2 anaphylatoxin chemotactic receptor binding ...Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Peptide ligand-binding receptors / vascular associated smooth muscle cell differentiation / 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 / positive regulation of phagocytosis, engulfment / positive regulation of developmental growth / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / G alpha (i) signalling events / Neutrophil degranulation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / response to magnesium ion / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / response to glucocorticoid / positive regulation of phagocytosis / response to progesterone / fatty acid metabolic process / response to bacterium / positive regulation of receptor-mediated endocytosis / response to estrogen / positive regulation of angiogenesis / chemotaxis / response to estradiol / positive regulation of protein phosphorylation / retina development in camera-type eye / positive regulation of ERK1 and ERK2 cascade / inflammatory response / receptor ligand activity / response to xenobiotic stimulus / lipid binding / cell surface / protein-containing complex / extracellular space / extracellular region
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 / : / 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 / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZanotti, G. / Bassetto, A. / Battistutta, R. / Stoppini, M. / Folli, C. / Berni, R.
Citation
Journal: Biochim.Biophys.Acta / Year: 2000
Title: Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment.
Authors: Zanotti, G. / Bassetto, A. / Battistutta, R. / Folli, C. / Arcidiaco, P. / Stoppini, M. / Berni, R.
#1: Journal: Science / Year: 1998
Title: X-ray Crystal Structure of C3d: A C3 Fragment and Ligand for Complement Receptor 2
Authors: Nagar, B. / Jones, R.G. / Diefenbach, R.J. / Isenman, D.E. / Rini, J.M.
History
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT C3 PRECURSOR
B: COMPLEMENT C3 PRECURSOR
C: COMPLEMENT C3 PRECURSOR
D: COMPLEMENT C3 PRECURSOR


Theoretical massNumber of molelcules
Total (without water)124,6064
Polymers124,6064
Non-polymers00
Water7,314406
1
A: COMPLEMENT C3 PRECURSOR
B: COMPLEMENT C3 PRECURSOR


Theoretical massNumber of molelcules
Total (without water)62,3032
Polymers62,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-3 kcal/mol
Surface area20690 Å2
MethodPISA
2
C: COMPLEMENT C3 PRECURSOR
D: COMPLEMENT C3 PRECURSOR


Theoretical massNumber of molelcules
Total (without water)62,3032
Polymers62,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-3 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.62, 99.93, 114.88
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
COMPLEMENT C3 PRECURSOR / C3DG


Mass: 31151.398 Da / Num. of mol.: 4 / Fragment: N-TERMINALLY TRUNCATED C3DG FRAGMENT / Mutation: M1081Y, W1082V, S1085V / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: PLASMA / References: UniProt: P01026
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25%-30% PEG 6000, 0.05 M POTASSIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 15 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
20.01 MTris-HCl1drop
325-30 %(w/v)PEG60001reservoir
40.05 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→55 Å / Num. all: 64362 / Num. obs: 64362 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.3
Reflection shellResolution: 1.94→2.17 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.083 / % possible all: 77.1
Reflection shell
*PLUS
% possible obs: 77.1 % / Num. unique obs: 18274 / Mean I/σ(I) obs: 8.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.9→55 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER / Details: REFLECTIONS WITH FOBS<2.5 FCALC WERE EXCLUDED FROM REFINEMENT
RfactorNum. reflection
Rfree0.253 5952
Rwork0.212 -
obs0.212 60237
all-64312
Refinement stepCycle: LAST / Resolution: 1.9→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8756 0 0 406 9162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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