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- PDB-4p3b: Crystal structure of the mouse C5a-desArg anaphylatoxin -

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Basic information

Entry
Database: PDB / ID: 4p3b
TitleCrystal structure of the mouse C5a-desArg 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: 2.1 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.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Nov 6, 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)36,25219
Polymers35,5624
Non-polymers69015
Water3,675204
1
A: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0284
Polymers8,8901
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0284
Polymers8,8901
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2138
Polymers8,8901
Non-polymers3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9823
Polymers8,8901
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Complement C5
C: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,24112
Polymers17,7812
Non-polymers46010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-5 kcal/mol
Surface area8480 Å2
MethodPISA
6
B: Complement C5
hetero molecules

D: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0117
Polymers17,7812
Non-polymers2305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2060 Å2
ΔGint-6 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.210, 55.210, 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: 8890.376 Da / Num. of mol.: 4 / Fragment: UNP residues 679-754
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.: 15 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
PH range: 4.0 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20489 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 23.65 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.123 / Χ2: 0.97 / Net I/σ(I): 14.62 / Num. measured all: 131068
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
2.1-2.26.40.8850.6622.9516956265626550.722100
2.2-2.30.9270.5113.8414392224622460.558100
2.3-2.40.9380.4044.8811955186418640.441100
2.4-2.50.9550.3345.7910046156715660.36599.9
2.5-2.70.9760.2467.5615986249124910.269100
2.7-2.90.9890.1710.6411998185518550.186100
2.9-3.20.9910.12414.612782198219810.13699.9
3.2-3.50.9960.07422.778885138713860.08199.9
3.5-40.9980.0532.729281145714550.05599.9
4-4.50.9980.04137.4655528858810.04599.5
4.5-50.9980.03840.336605785770.04299.8
5-60.9980.04136.5140466436420.04599.8
6-80.9990.03539.4832465155140.03899.8
8-100.9990.02448.8111561861850.02699.5
10-1510.02450.197991331310.02698.5
15-2010.02149.1220837370.024100
20-3010.0244.5310219180.02294.7
300.9980.04217.2418750.04971.4

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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: 1.8.3_1479)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3A

4p3a


Resolution: 2.1→32.509 Å / FOM work R set: 0.842 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1044 5.13 %random
Rwork0.1803 19306 --
obs0.1825 20350 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.78 Å2 / Biso mean: 35.78 Å2 / Biso min: 12.99 Å2
Refinement stepCycle: final / Resolution: 2.1→32.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 45 204 2461
Biso mean--52.22 38.33 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032286
X-RAY DIFFRACTIONf_angle_d0.7113021
X-RAY DIFFRACTIONf_chiral_restr0.029330
X-RAY DIFFRACTIONf_plane_restr0.003388
X-RAY DIFFRACTIONf_dihedral_angle_d13.645874
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 (%)
2.1001-2.21080.26751520.2252763291599
2.2108-2.34920.2711360.19872719285599
2.3492-2.53060.2491670.19862727289499
2.5306-2.78510.22531340.195327782912100
2.7851-3.18780.25971580.19282732289099
3.1878-4.01510.18971510.160927742925100
4.0151-32.51310.19851460.16092813295999
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)
13.1082-0.7499-0.33412.8490.253.01660.02870.10840.1525-0.1276-0.11240.1521-0.3872-0.5850.03570.18170.0505-0.02110.2615-0.01340.147718.4258-25.71014.2084
24.21380.76420.6754.99440.30693.4872-0.1896-0.0340.29370.28140.1169-0.0617-0.7370.14150.03980.2809-0.0014-0.02720.1403-0.00250.19453.152-46.06492.7554
33.5887-1.91910.06264.15360.73343.45440.0005-0.1013-0.0803-0.08370.0467-0.2760.12140.5185-0.06620.13260.00730.00180.2117-0.00170.164738.9168-32.7164.6224
44.5318-0.1417-0.64625.22480.10164.6636-0.0413-0.0465-0.55210.26930.03570.30670.7646-0.23920.03360.2965-0.0146-0.01790.14050.03470.2971-0.6832-11.98370.5919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA677 - 745
2X-RAY DIFFRACTION2chain BB678 - 746
3X-RAY DIFFRACTION3chain CC677 - 746
4X-RAY DIFFRACTION4chain DD678 - 745

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