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- PDB-4i6o: Crystal structure of chemically synthesized human anaphylatoxin C3a -

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Basic information

Entry
Database: PDB / ID: 4i6o
TitleCrystal structure of chemically synthesized human anaphylatoxin C3a
ComponentsComplement C3
KeywordsIMMUNE SYSTEM / disulfide-rich / alpha-helical bundle / drumstick / complement system / third component of complement (C3) / local inflammatory process mediator / smooth muscle contraction induction / vascular permeability increase / mast cell histamine release / C3a receptor / GPCR / extracellular / blood plasma
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / 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 G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / 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 G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / 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 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWang, C.I.A. / Ghassemian, A. / Collins, B. / Lewis, R.J. / Alewood, P.F. / Durek, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2013
Title: Efficient chemical synthesis of human complement protein C3a.
Authors: Ghassemian, A. / Wang, C.I. / Yau, M.K. / Reid, R.C. / Lewis, R.J. / Fairlie, D.P. / Alewood, P.F. / Durek, T.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2332
Polymers9,1151
Non-polymers1181
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.285, 68.285, 39.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Complement C3


Mass: 9114.731 Da / Num. of mol.: 1 / Fragment: C3a anaphylatoxin (UNP residues 672-748) / Source method: obtained synthetically
Details: native chemical ligation of three polypeptide segments
Source: (synth.) Homo sapiens (human) / References: UniProt: P01024
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION, HANGING DROP, 1 uL 5 mg/mL lyophilized C3a in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic, 49-51% v/v MPD, pH 8.5) against ...Details: VAPOR DIFFUSION, HANGING DROP, 1 uL 5 mg/mL lyophilized C3a in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic, 49-51% v/v MPD, pH 8.5) against 500 uL reservoir, prepared at 277K, incubated at 281K for 96 hours, stored at 277K, rhomboid-shaped crystals appeared after 6 days and grew to a final size of 0.5 x 0.2 x 0.2 mm

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.14→39.27 Å / Num. obs: 5870 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 22.1 % / Biso Wilson estimate: 61.793 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.9
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 22 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→19.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.335 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.228 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26793 946 16.2 %RANDOM
Rwork0.20845 ---
all0.21839 5870 --
obs0.21839 4899 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.04 Å20 Å2
2---0.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.14→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 0 8 19 584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019575
X-RAY DIFFRACTIONr_bond_other_d0.0010.02576
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.986766
X-RAY DIFFRACTIONr_angle_other_deg0.8953.0091310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.943567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64320.6929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.81915115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5541510
X-RAY DIFFRACTIONr_chiral_restr0.1110.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 70 -
Rwork0.262 369 -
obs-369 100 %

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