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- PDB-6jv8: Crystal structure of Rat C5a -

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Basic information

Entry
Database: PDB / ID: 6jv8
TitleCrystal structure of Rat C5a
ComponentsComplement C5Complement component 5
KeywordsIMMUNE SYSTEM / Agonist / C5aR / Immune
Function / homology
Function and homology information


C5a anaphylatoxin chemotactic receptor binding / : / negative regulation of norepinephrine secretion / membrane attack complex / negative regulation of dopamine secretion / inflammatory response to wounding / cytolysis / leukocyte migration involved in inflammatory response / positive regulation of chemotaxis / negative regulation of macrophage chemotaxis ...C5a anaphylatoxin chemotactic receptor binding / : / negative regulation of norepinephrine secretion / membrane attack complex / negative regulation of dopamine secretion / inflammatory response to wounding / cytolysis / leukocyte migration involved in inflammatory response / positive regulation of chemotaxis / negative regulation of macrophage chemotaxis / glomerulus development / neutrophil homeostasis / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / complement activation, classical pathway / kidney development / intracellular calcium ion homeostasis / positive regulation of angiogenesis / chemotaxis / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / in utero embryonic development / inflammatory response / extracellular space
Similarity search - Function
Complement C5 / Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...Complement C5 / Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / 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
Complement C5 / Complement C5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.582 Å
AuthorsZuo, C.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China21532004 China
National Natural Science Foundation of China91753205 China
National Natural Science Foundation of China81621002 China
National Natural Science Foundation of China21621003 China
CitationJournal: To Be Published
Title: Chimeric protein probes for C5a receptors through fusion of anaphylatoxin C5a core region with a small-molecule antagonist
Authors: Zuo, C.
History
DepositionApr 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,8871
Polymers8,8871
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5840 Å2
Unit cell
Length a, b, c (Å)26.250, 36.870, 41.490
Angle α, β, γ (deg.)90.39, 105.09, 95.77
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein Complement C5 / Complement component 5 / anaphylatoxin C5a


Mass: 8887.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P08650, UniProt: A0A096P6L9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.02M CaCl2, 0.02M CdCl2, 0.02M CoCl2, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.582→50 Å / Num. obs: 13647 / % possible obs: 89 % / Redundancy: 1.1 % / Net I/σ(I): 11
Reflection shellResolution: 1.582→1.85 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 1.582→25.202 Å / SU ML: 0.09 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.78
RfactorNum. reflection% reflection
Rfree0.2736 740 5.42 %
Rwork0.229 --
obs0.2314 13647 66.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.582→25.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms613 0 0 145 758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006626
X-RAY DIFFRACTIONf_angle_d0.73838
X-RAY DIFFRACTIONf_dihedral_angle_d17.204398
X-RAY DIFFRACTIONf_chiral_restr0.03788
X-RAY DIFFRACTIONf_plane_restr0.004108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5816-1.70370.5583180.3498427X-RAY DIFFRACTION11
1.7037-1.87510.33581180.27691998X-RAY DIFFRACTION51
1.8751-2.14630.32171970.24043298X-RAY DIFFRACTION86
2.1463-2.70360.27412100.22783538X-RAY DIFFRACTION92
2.7036-25.20530.23921970.21543646X-RAY DIFFRACTION94

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