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- PDB-5o9h: Crystal structure of thermostabilised human C5a anaphylatoxin che... -

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Basic information

Entry
Database: PDB / ID: 5o9h
TitleCrystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1 (C5aR) in complex with NDT9513727
ComponentsC5a anaphylatoxin chemotactic receptor 1
KeywordsMEMBRANE PROTEIN / GPCR / 7TM / SIGNALLING PROTEIN
Function / homology
Function and homology information


complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance ...complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / cellular defense response / neutrophil chemotaxis / Peptide ligand-binding receptors / secretory granule membrane / positive regulation of epithelial cell proliferation / Regulation of Complement cascade / astrocyte activation / G protein-coupled receptor activity / microglial cell activation / mRNA transcription by RNA polymerase II / cognition / positive regulation of angiogenesis / chemotaxis / apical part of cell / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / immune response / Neutrophil degranulation / signal transduction / plasma membrane
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-9P2 / CITRIC ACID / OLEIC ACID / L(+)-TARTARIC ACID / C5a anaphylatoxin chemotactic receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRobertson, N. / Rappas, M. / Dore, A.S. / Brown, J. / Bottegoni, G. / Koglin, M. / Cansfield, J. / Jazayeri, A. / Cooke, R.M. / Marshall, F.H.
CitationJournal: Nature / Year: 2018
Title: Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727.
Authors: Robertson, N. / Rappas, M. / Dore, A.S. / Brown, J. / Bottegoni, G. / Koglin, M. / Cansfield, J. / Jazayeri, A. / Cooke, R.M. / Marshall, F.H.
History
DepositionJun 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Source and taxonomy / Category: entity_src_gen / pdbx_related_exp_data_set / Item: _entity_src_gen.host_org_common_name
Revision 1.3Jan 17, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: 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: C5a anaphylatoxin chemotactic receptor 1
B: C5a anaphylatoxin chemotactic receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,31340
Polymers71,4852
Non-polymers10,82838
Water1,27971
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, CONCENTRATION DEPENDENT DYNAMIC EQUILIBRIUM OF MONOMER AND DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19400 Å2
ΔGint56 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.093, 51.096, 118.936
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein C5a anaphylatoxin chemotactic receptor 1 / C5a anaphylatoxin chemotactic receptor / C5aR


Mass: 35742.426 Da / Num. of mol.: 2
Mutation: S85A, I91A, I142A, N146R, A156L, F172A, R232A, A234E, L311E, S317E, N321E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5AR1, C5AR, C5R1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P21730

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-9P2 / 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine


Mass: 573.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H35N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical...
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.67 Å3/Da / Density % sol: 66.51 % / Description: ELONGATED PLATES
Crystal growTemperature: 295.65 K / Method: lipidic cubic phase / pH: 5.5
Details: 100mM tri-sodium citrate pH 5.5, 200mM Na/K tartrate, 35-45% (v/v) polyethylene glycol 400
PH range: 5.5 - 6.0 / Temp details: NONE

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: CONSTANT
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015
Details: OXFORD DANFYSIK/SESO TWO STAGE DEMAGNIFICATION USING TWO K-B PAIRS OF BIMORPH TYPE MIRRORS
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.7→34.6 Å / Num. obs: 26541 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.631 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DKL

4dkl


Resolution: 2.7→19.894 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1352 5.11 %RANDOM
Rwork0.2079 ---
obs0.2095 26440 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 616 71 5349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045377
X-RAY DIFFRACTIONf_angle_d1.0357173
X-RAY DIFFRACTIONf_dihedral_angle_d12.3261707
X-RAY DIFFRACTIONf_chiral_restr0.03800
X-RAY DIFFRACTIONf_plane_restr0.004859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79630.32111260.26952487X-RAY DIFFRACTION100
2.7963-2.90790.30981370.25542485X-RAY DIFFRACTION100
2.9079-3.03980.31031450.25392496X-RAY DIFFRACTION100
3.0398-3.19950.27161320.23232525X-RAY DIFFRACTION100
3.1995-3.3990.25411350.21952492X-RAY DIFFRACTION100
3.399-3.660.26951400.20992496X-RAY DIFFRACTION100
3.66-4.02550.20661280.18922518X-RAY DIFFRACTION99
4.0255-4.60170.21561420.1762526X-RAY DIFFRACTION99
4.6017-5.77410.22121410.19362521X-RAY DIFFRACTION99
5.7741-19.89490.18481260.1982542X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0280.00160.00320.0345-0.04180.0139-0.09870.21880.11620.00290.20730.153-0.0618-0.129300.13130.0295-0.03750.48890.0450.254675.5756-10.278822.7269
20.0457-0.0382-0.01370.0547-0.03430.0157-0.0143-0.10190.32850.1948-0.16470.3033-0.1103-0.115300.09110.1292-0.06690.20970.07780.131583.0024-4.505425.8745
30.14510.0098-0.0590.0595-0.00510.0186-0.03640.0171-0.007-0.022-0.029-0.0042-0.02070.022700.118-0.01250.00880.07880.00570.111596.0239-7.196633.3198
4-0.0029-0.0057-0.0012-0.0016-0.00240.0019-0.1178-0.0101-0.0850.0207-0.0712-0.08360.01240.045400.4250.2037-0.01490.53230.08360.330989.7821-8.17450.8123
50.08410.10350.02990.02230.08610.0215-0.0947-0.1304-0.20670.04020.26550.26770.11640.126900.0932-0.1195-0.0937-0.009-0.08740.046793.6305-21.782626.9243
60.0217-0.01850.04230.0873-0.02460.0093-0.0085-0.0939-0.0141-0.14030.0280.0404-0.0629-0.2008-00.15980.0202-0.00670.25180.03820.242879.7402-12.425238.1172
70.14520.22060.0420.2312-0.05970.0634-0.0218-0.0027-0.0636-0.0060.0271-0.01740.08430.13100.06560.01560.01920.0651-0.02630.085122.3792-8.415329.5939
80.01040.00980.015-0.00380.00450.0071-0.0039-0.0440.073-0.13-0.05430.0740.0356-0.078100.56-0.0358-0.04340.3842-0.01360.2337118.3155-8.49961.7192
9-0.00370.01580.00240.0015-0.01760.00530.0590.1209-0.0376-0.04460.0257-0.05020.04250.0492-00.1204-0.0006-0.01780.1374-0.01560.0985108.09341.765714.6525
100.11950.0804-0.08350.18230.03740.01110.0238-0.04830.1099-0.0910.0059-0.0587-0.04470.0828-00.12220.0110.02460.06530.0140.0793120.42877.365430.4197
110.04150.01240.02030.12090.04310.0066-0.00380.0284-0.1941-0.06460.2627-0.03680.0433-0.0049-00.13630.0832-0.01240.1857-0.01730.2234131.5627-4.991738.1479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 281 )
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 330 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 173 )
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 190 )
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 211 )
10X-RAY DIFFRACTION10chain 'B' and (resid 212 through 281 )
11X-RAY DIFFRACTION11chain 'B' and (resid 282 through 331 )

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