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- PDB-6c1r: Crystal structure of human C5a receptor in complex with an orthos... -

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Basic information

Entry
Database: PDB / ID: 6c1r
TitleCrystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist avacopan
Components
  • PMX53
  • Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
KeywordsMEMBRANE PROTEIN/INHIBITOR / GPCR / MEMBRANE PROTEIN-INHIBITOR complex
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 / activation of phospholipase C activity / positive regulation of vascular endothelial growth factor production / cellular defense response / Peptide ligand-binding receptors / neutrophil chemotaxis / secretory granule membrane / positive regulation of epithelial cell proliferation / Regulation of Complement cascade / G protein-coupled receptor activity / astrocyte activation / 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 / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / immune response / inflammatory response / iron ion binding / heme binding / Neutrophil degranulation / signal transduction / plasma membrane
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
PMX53 / avacopan / MALONATE ION / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / Soluble cytochrome b562 / C5a anaphylatoxin chemotactic receptor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLiu, H. / Wang, L. / Wei, Z. / Zhang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Orthosteric and allosteric action of the C5a receptor antagonists.
Authors: Liu, H. / Kim, H.R. / Deepak, R.N.V.K. / Wang, L. / Chung, K.Y. / Fan, H. / Wei, Z. / Zhang, C.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 5, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
L: PMX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,20613
Polymers48,4052
Non-polymers2,80211
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-9 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.411, 52.608, 83.865
Angle α, β, γ (deg.)90.000, 106.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BL

#1: Protein Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera / Cytochrome b-562 / C5a anaphylatoxin chemotactic receptor / C5aR


Mass: 47505.480 Da / Num. of mol.: 1
Fragment: cytochrome (UNP residues 23-127) + C5a receptor (UNP residues 30-331)
Mutation: M29W, H124I, R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, C5AR1, C5AR, C5R1 / Plasmid: pFastbac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P21730
#2: Protein/peptide PMX53


Type: Cyclic peptide / Mass: 899.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PMX53

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Non-polymers , 7 types, 56 molecules

#3: Chemical ChemComp-EFD / avacopan / (2R,3S)-2-[4-(cyclopentylamino)phenyl]-1-(2-fluoro-6-methylbenzene-1-carbonyl)-N-[4-methyl-3-(trifluoromethyl)phenyl]piperidine-3-carboxamide / Avacopan


Mass: 581.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35F4N3O2 / Comment: medication, inhibitor, antagonist*YM
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 283 K / Method: lipidic cubic phase / pH: 6.5
Details: 25-32% PEG300, 100 mM MES, pH6.5, 90-120 mM sodium malonate, 1% P400, 5 uM avacopan, 5 uM PMX53

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 25865 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.052 / Rrim(I) all: 0.138 / Χ2: 0.946 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.10.99812110.4550.5221.1330.65994.8
2.24-2.284.90.94512790.5180.4561.0550.65197.9
2.28-2.325.30.87312600.7250.3960.9630.6498.7
2.32-2.375.90.80612800.7440.3490.8820.65899.2
2.37-2.426.20.6813170.860.2880.7410.6399.7
2.42-2.486.60.62112430.8570.2540.6730.67199.6
2.48-2.546.90.57113020.8960.2290.6170.672100
2.54-2.616.80.45312980.9180.1830.4890.725100
2.61-2.687.40.37912870.9470.1470.4070.721100
2.68-2.777.30.31813190.9550.1240.3420.735100
2.77-2.877.50.2812730.9640.1070.3010.782100
2.87-2.997.40.23613050.9740.0910.2540.854100
2.99-3.127.50.20213140.9820.0780.2170.9599.9
3.12-3.297.40.16812860.9830.0660.1811.11799.9
3.29-3.497.30.13413000.9890.0520.1441.28699.9
3.49-3.767.20.11313080.9930.0450.1221.664100
3.76-4.147.40.0913020.9940.0360.0971.2799.8
4.14-4.736.20.07412950.9950.0320.0811.39498.6
4.73-5.967.30.07313240.9950.0290.0791.17799.8
5.96-306.90.06713620.9950.0280.0731.18299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZUD

4zud


Resolution: 2.2→27.359 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2235 1264 5.06 %
Rwork0.1923 --
obs0.1939 24988 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.8 Å2 / Biso mean: 50.596 Å2 / Biso min: 20.57 Å2
Refinement stepCycle: final / Resolution: 2.2→27.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 196 45 3087
Biso mean--59.8 40.09 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053102
X-RAY DIFFRACTIONf_angle_d1.0064200
X-RAY DIFFRACTIONf_chiral_restr0.028500
X-RAY DIFFRACTIONf_plane_restr0.004499
X-RAY DIFFRACTIONf_dihedral_angle_d16.9691104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.28810.28961430.26232561270498
2.2881-2.39220.27471320.2342617274999
2.3922-2.51820.23321450.212326182763100
2.5182-2.67580.21821420.186926172759100
2.6758-2.88220.22341340.179626542788100
2.8822-3.17190.22391430.182726162759100
3.1719-3.630.23481390.190526712810100
3.63-4.56990.21981430.175826452788100
4.5699-27.36130.20481430.196927252868100
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)
13.12770.22680.94869.92517.30786.3671-0.2125-0.2045-0.08450.0837-0.38050.90260.1342-0.64770.67120.2155-0.0325-0.02440.34740.04090.4346-14.36643.6881-37.2846
24.16670.2231-4.06791.81430.24116.2736-0.34180.3763-0.463-0.1778-0.15110.33960.4013-0.67810.41880.2239-0.0272-0.05040.26220.00050.3268-7.4133-2.6149-42.297
33.83791.7358-4.20061.8088-1.70668.1873-0.13570.1197-0.0611-0.1520.03760.14290.2027-0.4560.04890.2402-0.0027-0.03310.22050.00990.3031-0.6147-0.3595-37.2673
49.8847-8.1057-2.1087.9615-2.3982.0046-0.26430.1909-0.9075-0.7611-0.36870.42281.87630.23760.510.7084-0.00510.06290.6283-0.00290.658113.047-2.2271-62.8976
51.437-1.0429-0.76323.62661.879.909-0.1725-0.1023-0.12660.2467-0.03640.29290.4797-0.09690.17770.1984-0.02290.00040.16190.02690.27233.3137-6.5401-33.5986
67.18913.5175-5.18573.434-2.66029.40540.1243-1.2552-0.57220.8491-0.4552-0.201-0.25980.7640.2490.4970.0303-0.00730.35580.06970.33593.91452.7249-20.2858
76.9298-0.31052.02755.4067-0.80482.1047-0.13060.9380.1906-0.7645-0.1927-0.05530.16050.11570.26690.3192-0.04880.02330.3441-0.00860.250910.098113.2462-53.2813
81.31580.35630.01671.80691.31145.9045-0.1231-0.05190.08880.0178-0.03360.2239-0.1685-0.12070.17790.19560.0481-0.01940.18730.03470.3328-2.298410.8855-35.0153
92.02460.2562-7.57283.1961.32479.50370.22351.0624-0.4686-0.4094-0.08260.4131-0.3321-0.4982-0.02930.50550.0241-0.17580.7121-0.01720.6522-11.10192.7421-59.698
107.05291.47963.69833.829-0.60623.0745-0.01361.0447-0.2053-1.14120.1771-0.187-0.3652-0.6067-0.11490.90720.01270.12961.0657-0.19390.4423-6.357917.7385-3.2386
112.00060.83575.58051.7833-0.25363.513-0.1844-1.31030.39690.3662-0.15710.5971-0.1205-1.8260.30770.7072-0.08560.19361.0935-0.26420.5194-9.718716.09846.99
122.01133.24917.38735.91371.25035.34970.1044-0.1261-0.61730.65650.1077-0.02350.5947-0.8169-0.24460.917-0.13230.14680.8016-0.28090.6033-6.19718.8653.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 65 )A30 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 97 )A66 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 139 )A98 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 149 )A140 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 180 )A150 - 180
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 211 )A181 - 211
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 237 )A212 - 237
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 305 )A238 - 305
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 327 )A306 - 327
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 68 )B12 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 90 )B69 - 90
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 110 )B91 - 110

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