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- PDB-4p3a: Crystal structure of the mouse C5a anaphylatoxin -

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Basic information

Entry
Database: PDB / ID: 4p3a
TitleCrystal structure of the mouse C5a anaphylatoxin
ComponentsComplement C5
KeywordsIMMUNE SYSTEM / complement anaphylatoxin / C5a / four-helix bundle / GPCR agonist
Function / homology
Function and homology information


Terminal pathway of complement / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / membrane attack complex / G alpha (i) signalling events / complement activation, alternative pathway / endopeptidase inhibitor activity / complement activation, classical pathway / positive regulation of angiogenesis ...Terminal pathway of complement / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / membrane attack complex / G alpha (i) signalling events / complement activation, alternative pathway / endopeptidase inhibitor activity / complement activation, classical pathway / positive regulation of angiogenesis / killing of cells of another organism / in utero embryonic development / inflammatory response / extracellular space
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 domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain ...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 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 / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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
FORMIC ACID / Complement C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsYatime, L. / Schatz-Jakobsen, J.A. / 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 1.2Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.country / _citation.journal_id_ASTM ..._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 1.3Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
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: Complement C5
B: Complement C5
C: Complement C5
D: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,92720
Polymers36,1904
Non-polymers73616
Water5,999333
1
A: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1864
Polymers9,0481
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3708
Polymers9,0481
Non-polymers3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1403
Polymers9,0481
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2325
Polymers9,0481
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Complement C5
B: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,55512
Polymers18,0952
Non-polymers46010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-6 kcal/mol
Surface area8390 Å2
MethodPISA
6
C: Complement C5
D: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3718
Polymers18,0952
Non-polymers2766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-6 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.950, 54.950, 117.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
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 / Hemolytic complement


Mass: 9047.569 Da / Num. of mol.: 4 / Fragment: UNP residues 679-755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C5, Hc / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 Express / References: UniProt: P06684
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: 0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15
PH range: 3.5 - 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 68172 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 12.02 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.073 / Χ2: 0.995 / Net I/σ(I): 15.1 / Num. measured all: 284826
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
1.4-1.54.10.760.7422.335257912762127390.84999.8
1.5-1.60.9020.4024.2340479974897320.45999.8
1.6-1.70.950.278631711758375750.31899.9
1.7-1.80.9730.2057.9925235600460000.23499.9
1.8-20.9890.13311.6536777870186920.15299.9
2-2.50.9970.05724.314830911455114410.06599.9
2.5-30.9980.03832.9221290505050440.04499.9
3-3.50.9990.02941.9610692257225680.03399.8
3.5-40.9990.02447.65881143914360.02899.8
4-50.9990.02449.015971147014640.02799.6
5-60.9990.02348.0325306296250.02799.4
6-80.9990.02248.8220655085070.02599.8
8-100.9990.0247.316711861780.02495.7
10-120.9990.01748.4125376690.0290.8
12-150.9990.0251.3820660530.02388.3
15-2010.01948.7911934320.02294.1
2010.0242.15826170.02265.4

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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: dev_1593)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CU7

3cu7


Resolution: 1.4→36.889 Å / FOM work R set: 0.9068 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3452 5.06 %random
Rwork0.1442 64713 --
obs0.1457 68165 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65 Å2 / Biso mean: 20.19 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: final / Resolution: 1.4→36.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 48 333 2593
Biso mean--23.44 29.91 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082445
X-RAY DIFFRACTIONf_angle_d1.1983260
X-RAY DIFFRACTIONf_chiral_restr0.065351
X-RAY DIFFRACTIONf_plane_restr0.007428
X-RAY DIFFRACTIONf_dihedral_angle_d13.726943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41920.28791430.239225952738100
1.4192-1.43950.25411560.22326052761100
1.4395-1.4610.27871260.195225492675100
1.461-1.48380.21111420.183926062748100
1.4838-1.50810.21951480.161125452693100
1.5081-1.53410.19311310.150226072738100
1.5341-1.5620.17691520.136425712723100
1.562-1.59210.17641280.127225942722100
1.5921-1.62460.14151270.12925982725100
1.6246-1.65990.16971640.119825852749100
1.6599-1.69850.13741340.114725592693100
1.6985-1.7410.14921280.115325752703100
1.741-1.78810.17691420.118625892731100
1.7881-1.84070.17411450.128525792724100
1.8407-1.90010.14331390.128125872726100
1.9001-1.9680.15041400.126525842724100
1.968-2.04680.15021140.125426232737100
2.0468-2.13990.16121310.12525752706100
2.1399-2.25270.15481370.122225722709100
2.2527-2.39380.1611290.122926452774100
2.3938-2.57860.1711280.13625702698100
2.5786-2.8380.18191500.151826082758100
2.838-3.24850.19911380.166226042742100
3.2485-4.09190.15721450.144525802725100
4.0919-36.90140.18071350.16792608274399

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