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- PDB-1qqf: N-TERMINALLY TRUNCATED C3D,G FRAGMENT OF THE COMPLEMENT SYSTEM -

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Basic information

Entry
Database: PDB / ID: 1qqf
TitleN-TERMINALLY TRUNCATED C3D,G FRAGMENT OF THE COMPLEMENT SYSTEM
ComponentsPROTEIN (COMPLEMENT C3DG)
KeywordsIMMUNE SYSTEM / ALPHA-ALPHA BARREL / COMPLEMENT
Function / homology
Function and homology information


Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / tolerance induction / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / tolerance induction / 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 lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of developmental growth / 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 / innervation / 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 progesterone / positive regulation of phagocytosis / response to glucocorticoid / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / response to estrogen / positive regulation of protein phosphorylation / positive regulation of angiogenesis / chemotaxis / response to estradiol / retina development in camera-type eye / positive regulation of ERK1 and ERK2 cascade / receptor ligand activity / response to xenobiotic stimulus / inflammatory response / innate immune response / 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 / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsZanotti, G. / Bassetto, A. / Battistutta, R. / Stoppini, M. / 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 4, 1999Deposition site: RCSB / Processing site: NDB
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 1.3Jan 21, 2015Group: Refinement description
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (COMPLEMENT C3DG)


Theoretical massNumber of molelcules
Total (without water)31,1671
Polymers31,1671
Non-polymers00
Water5,945330
1
A: PROTEIN (COMPLEMENT C3DG)

A: PROTEIN (COMPLEMENT C3DG)


Theoretical massNumber of molelcules
Total (without water)62,3352
Polymers62,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)68.430, 68.430, 117.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-85-

HOH

Detailsdimer generated from the monomer of the asymmetric unit and a second monomer related to the first by a crystallographic twofold axis

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Components

#1: Protein PROTEIN (COMPLEMENT C3DG)


Mass: 31167.398 Da / Num. of mol.: 1 / Fragment: N-TERMINALLY TRUNCATED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: PLASMA / References: UniProt: P01026
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growpH: 7 / Details: 24% PEG 6000, K PHOSPHATE 50 MM, pH 7.0
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
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: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→26.9 Å / Num. obs: 50041 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.04
Reflection shellResolution: 1.45→1.62 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.285 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 % / Num. unique obs: 13685 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.45→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC B FACTORS IN THE LAST CYCLES
RfactorNum. reflectionSelection details
Rfree0.217 2487 RANDOM
all0.164 49740 -
obs0.161 --
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 330 2528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.9

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