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- PDB-3hqb: Crystal structure of human desarg-C5A -

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Basic information

Entry
Database: PDB / ID: 3hqb
TitleCrystal structure of human desarg-C5A
ComponentsComplement C5
KeywordsIMMUNE SYSTEM / COMPLEMENT / C5A / ANAPHYLATOXIN / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Cytolysis / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Membrane attack complex / Secreted
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 / positive regulation of chemokine production / Peptide ligand-binding receptors ...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 / positive regulation of chemokine production / Peptide ligand-binding receptors / complement activation, classical pathway / 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. / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.299 Å
AuthorsCook, W.J. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of human desArg-C5a.
Authors: Cook, W.J. / Galakatos, N. / Boyar, W.C. / Walter, R.L. / Ealick, S.E.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C5
B: Complement C5


Theoretical massNumber of molelcules
Total (without water)16,3232
Polymers16,3232
Non-polymers00
Water00
1
A: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,1621
Polymers8,1621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5


Theoretical massNumber of molelcules
Total (without water)8,1621
Polymers8,1621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-14 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.720, 54.720, 96.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 20:29 )
211chain B and (resseq 20:29 )
112chain A and (resseq 31:34 )
212chain B and (resseq 31:34 )
113chain A and (resseq 36:41 )
213chain B and (resseq 36:41 )
114chain A and (resseq 43:45 )
214chain B and (resseq 43:45 )
115chain A and (resseq 47:52 )
215chain B and (resseq 47:52 )
116chain A and (resseq 54:61 )
216chain B and (resseq 54:61 )
117chain A and (resseq 63:63 )
217chain B and (resseq 63:63 )

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / ...C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / Complement C5 alpha chain / C5a anaphylatoxin / Complement C5 alpha' chain


Mass: 8161.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE SYNTHETIC C5A GENE OF PB-6 REPLACES THE N-TERMINAL THREONINE RESIDUE OF HUMAN C5A WITH METHIONINE.
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Plasmid: pB-6 / Production host: Escherichia coli (E. coli) / Strain (production host): LCIQ / References: UniProt: P01031

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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: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2.4 M sodium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 19, 1991
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.299→26.3 Å / Num. all: 2760 / Num. obs: 2707 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
PHASERphasing
CNS1.2refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HQA

3hqa


Resolution: 3.299→23.799 Å / SU ML: 0.51 / Isotropic thermal model: RESTRAINED / σ(F): 2 / Phase error: 30.2 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.3069 217 9.49 %
Rwork0.2099 --
obs0.2191 2287 83.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.606 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å20 Å20 Å2
2--4.14 Å20 Å2
3----8.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.299→23.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 0 957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012973
X-RAY DIFFRACTIONf_angle_d1.5161295
X-RAY DIFFRACTIONf_dihedral_angle_d19.347369
X-RAY DIFFRACTIONf_chiral_restr0.081149
X-RAY DIFFRACTIONf_plane_restr0.008167
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A71X-RAY DIFFRACTIONPOSITIONAL
12B71X-RAY DIFFRACTIONPOSITIONAL0.091
21A30X-RAY DIFFRACTIONPOSITIONAL
22B30X-RAY DIFFRACTIONPOSITIONAL0.039
31A49X-RAY DIFFRACTIONPOSITIONAL
32B49X-RAY DIFFRACTIONPOSITIONAL0.047
41A19X-RAY DIFFRACTIONPOSITIONAL
42B19X-RAY DIFFRACTIONPOSITIONAL0.047
51A46X-RAY DIFFRACTIONPOSITIONAL
52B46X-RAY DIFFRACTIONPOSITIONAL0.052
61A54X-RAY DIFFRACTIONPOSITIONAL
62B54X-RAY DIFFRACTIONPOSITIONAL0.059
71A6X-RAY DIFFRACTIONPOSITIONAL
72B6X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2986-4.15230.3449880.209871X-RAY DIFFRACTION72
4.1523-23.79930.29111290.21041199X-RAY DIFFRACTION94
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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