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- PDB-4p39: Crystal structure of the human C5aR antagonist C5a-A8 -

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Basic information

Entry
Database: PDB / ID: 4p39
TitleCrystal structure of the human C5aR antagonist C5a-A8
ComponentsComplement C5
KeywordsIMMUNE SYSTEM / complement anaphylatoxin / C5a / three-helix bundle / GPCR antagonist
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / 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 / 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. / 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 / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / molecular replacement / Resolution: 2.401 Å
AuthorsYatime, L. / Schatz-Jakobsen, J.A. / Larsen, C. / Andersen, G.R.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: Structural and functional characterization of human and murine C5a anaphylatoxins.
Authors: Schatz-Jakobsen, J.A. / Yatime, L. / Larsen, C. / Petersen, S.V. / Klos, A. / Andersen, G.R.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _chem_comp.formula / _chem_comp.id ..._chem_comp.formula / _chem_comp.id / _chem_comp.name / _citation.country / _citation.journal_id_ASTM / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.2Oct 16, 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: Complement C5
B: Complement C5
C: Complement C5
D: Complement C5


Theoretical massNumber of molelcules
Total (without water)33,4634
Polymers33,4634
Non-polymers00
Water39622
1
A: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,3661
Polymers8,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,3661
Polymers8,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,3661
Polymers8,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,3661
Polymers8,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Complement C5
B: Complement C5

D: Complement C5

C: Complement C5


Theoretical massNumber of molelcules
Total (without water)33,4634
Polymers33,4634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area4210 Å2
ΔGint-42 kcal/mol
Surface area19290 Å2
MethodPISA
6
A: Complement C5

D: Complement C5


Theoretical massNumber of molelcules
Total (without water)16,7312
Polymers16,7312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1460 Å2
ΔGint-16 kcal/mol
Surface area10210 Å2
MethodPISA
7
B: Complement C5

C: Complement C5


Theoretical massNumber of molelcules
Total (without water)16,7312
Polymers16,7312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area1570 Å2
ΔGint-16 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.350, 83.240, 119.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit (chains A, B, C & D)

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Components

#1: Protein
Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 8365.678 Da / Num. of mol.: 4 / Fragment: UNP residues 678-743 / Mutation: C704R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 Express / References: UniProt: P01031
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% 2-propanol, 20% PEG 4000, 0.1 M Na citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13812 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 50 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.088 / Χ2: 1.017 / Net I/σ(I): 17.07 / Num. measured all: 85853
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.56.10.9030.5523.819381156415410.60498.5
2.5-2.60.9590.4225.438888134913460.45999.8
2.6-2.70.9740.3277.047301114611440.35699.8
2.7-2.90.9860.22310.3711249183918380.24399.9
2.9-3.20.9940.16315.8313519201720100.17799.7
3.2-3.50.9950.11820.918735135813580.128100
3.5-40.9950.09824.028621147114690.10899.9
4-4.50.9980.05430.9956509129100.05999.8
4.5-50.9980.0533.0134135815800.05499.8
5-60.9980.04930.8637826696670.05499.7
6-70.9970.04532.9220673433420.04999.7
7-80.9970.04334.7611261921910.04899.5
8-90.9990.03834.956581231190.04296.7
9-100.9980.03835.3937176710.04293.4
10-150.9960.04334.137631551530.04898.7
15-200.9990.05232.8420742420.056100
20-300.9980.05630.8110023230.071100
300.9980.03226.28221280.0466.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQA

3hqa


Resolution: 2.401→48.644 Å / FOM work R set: 0.789 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 1023 7.62 %random
Rwork0.2236 12409 --
obs0.2247 13432 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.05 Å2 / Biso mean: 68.09 Å2 / Biso min: 28.72 Å2
Refinement stepCycle: final / Resolution: 2.401→48.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 0 22 2165
Biso mean---61.3 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022175
X-RAY DIFFRACTIONf_angle_d0.4632890
X-RAY DIFFRACTIONf_chiral_restr0.019331
X-RAY DIFFRACTIONf_plane_restr0.002368
X-RAY DIFFRACTIONf_dihedral_angle_d12.943838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4011-2.52770.33391410.27361661180293
2.5277-2.6860.31991640.27781711187596
2.686-2.89340.281430.25891734187797
2.8934-3.18450.331390.26711784192398
3.1845-3.64520.23041360.23661807194399
3.6452-4.5920.21861320.20071825195799
4.592-48.65440.19381680.19621887205599
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)
19.58322.28472.64790.73690.53374.0155-0.10080.3520.3275-0.09040.15290.12990.0106-0.2248-0.04730.2743-0.03410.04610.3842-0.00660.4154-18.2692-4.6303-33.7529
28.9387-5.6177-3.44178.43995.00265.5574-0.489-0.3008-0.48250.72670.10730.42430.2041-0.15180.2950.34870.03050.10820.39420.04190.4356-17.6707-1.3487-18.9607
32.0604-2.62160.64059.96392.20645.57170.43490.078-0.3562-0.0948-0.23230.492-0.0147-0.0986-0.15050.7570.04640.01210.3935-0.05640.49694.0642-17.8306-3.602
44.1721-2.56111.58769.3821-1.99645.16440.24060.43350.24130.0737-0.4369-0.83480.50990.18840.23230.42880.07910.04650.37970.06010.3627-29.7003-22.5699-10.195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA677 - 745
2X-RAY DIFFRACTION2chain BB677 - 745
3X-RAY DIFFRACTION3chain CC678 - 746
4X-RAY DIFFRACTION4chain DD678 - 745

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