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- PDB-7bag: C3b in complex with CP40 -

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Basic information

Entry
Database: PDB / ID: 7bag
TitleC3b in complex with CP40
Components
  • (Complement C3) x 2
  • Compstatin CP40
KeywordsIMMUNE SYSTEM / Complement system / C3b / C3 convertase / Inhibitor
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / 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
Similarity search - Domain/homology
ACETAMIDE / AMINO GROUP / DI(HYDROXYETHYL)ETHER / Complement C3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLamers, C. / Xue, X. / Smiesko, M. / van Son, H. / Wagner, B. / Sfyroera, G. / Gros, P. / Lambris, J. / Ricklin, D.
Funding support Switzerland, Netherlands, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_176104 Switzerland
Netherlands Organisation for Scientific Research (NWO)700.54.304 Netherlands
European Research Council (ERC)233229 Netherlands
European Communitys Seventh Framework Programme283570 Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: Insight into mode-of-action and structural determinants of the compstatin family of clinical complement inhibitors.
Authors: Lamers, C. / Xue, X. / Smiesko, M. / van Son, H. / Wagner, B. / Berger, N. / Sfyroera, G. / Gros, P. / Lambris, J.D. / Ricklin, D.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
B: Complement C3
C: Compstatin CP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,33112
Polymers177,2613
Non-polymers1,0709
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-43 kcal/mol
Surface area69840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.508, 90.528, 140.093
Angle α, β, γ (deg.)90.000, 108.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 71393.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide Compstatin CP40


Mass: 1794.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-4-deoxy-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 933 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#8: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 6.66% w/v polyethylene glycol 8000, 66.6 mM sodium chloride and 33.3 mM disodium phosphate/citric acid pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→48.03 Å / Num. obs: 159033 / % possible obs: 98.3 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.054 / Rrim(I) all: 0.111 / Net I/σ(I): 8.7 / Num. measured all: 666117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.034.31.9613309177470.3731.0772.2430.897.4
10.95-48.033.80.049392810250.9940.0280.05626.297.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.3.8data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WII

2wii


Resolution: 2→47.82 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 7834 4.93 %
Rwork0.1942 151101 -
obs0.1957 158935 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.04 Å2 / Biso mean: 55.228 Å2 / Biso min: 21.69 Å2
Refinement stepCycle: final / Resolution: 2→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12424 0 68 925 13417
Biso mean--71.8 52.75 -
Num. residues----1459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.020.34922670.3448489597
2.02-2.050.3642570.3376496597
2.05-2.070.32782700.3215493797
2.07-2.10.32392560.3074498997
2.1-2.130.31922650.293499797
2.13-2.150.31892490.2808497697
2.15-2.190.26612480.2823494097
2.19-2.220.31462600.277501398
2.22-2.250.30472310.2695504198
2.25-2.290.27592350.254502898
2.29-2.330.27682540.2538501498
2.33-2.370.292540.235502198
2.37-2.420.27362590.2299506098
2.42-2.470.26372560.2196497498
2.47-2.520.23932530.205507598
2.52-2.580.25522630.2076501298
2.58-2.640.24062800.1985500898
2.64-2.710.25622760.1965503198
2.71-2.790.22452780.1996506398
2.79-2.880.21532550.192504598
2.88-2.990.22232570.1891509199
2.99-3.110.21032610.1916503399
3.11-3.250.22492720.1897508199
3.25-3.420.20532740.1817506199
3.42-3.630.19952810.1735508299
3.63-3.910.18762740.1634503198
3.91-4.310.2052360.1562511799
4.31-4.930.16622530.1429514199
4.93-6.210.19722660.1703515299
6.21-47.820.2332940.1981522899
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)
13.8984-2.27770.34216.65560.93871.5330.16190.104-0.06890.3466-0.06780.4259-0.0277-0.8112-0.11040.31910.0011-0.0370.89260.11870.4553-20.7621-3.52667.632
22.86-1.31541.22042.9156-1.27633.28340.0410.1302-0.44450.03240.2450.80990.3515-0.8521-0.2930.3166-0.10630.02870.49050.01060.4702-5.1463-18.839837.5505
31.7179-0.5293-0.77712.77830.82736.19960.01410.1580.05150.0775-0.1028-0.04890.3139-0.1710.07130.1840.0016-0.0180.1883-0.00290.247828.8154-27.819929.5917
47.5997-1.95454.41051.8359-1.33784.9511-0.00890.62560.0239-0.2381-0.02090.05640.14880.17210.08330.27920.03740.04160.45110.0930.345817.5181-10.47371.3563
52.20460.61560.13352.3060.54552.1147-0.04370.35290.353-0.19190.16410.1061-0.4666-0.23560.02250.32920.0645-0.0760.52650.1820.49870.21913.76790.5344
61.4506-0.27291.01171.563-0.72763.5894-0.39170.07090.34350.47940.15140.0349-0.8124-0.3290.25850.50920.0905-0.08740.3013-0.02840.35878.2414-1.201243.9549
71.3276-1.26152.61720.9355-2.02626.15830.13450.088-0.0201-0.10220.05540.18970.2932-0.4927-0.21390.3066-0.0719-0.07750.52480.07130.3837-1.8213-12.258513.2849
82.71831.5854-0.02853.1592-1.050.9571-0.1305-0.12370.12090.37710.08030.0411-0.2051-0.07570.07310.52850.0814-0.02350.2166-0.04040.226421.2216-24.634464.0584
93.37930.36580.82522.8586-0.43246.2244-0.0863-0.08260.05280.0737-0.0975-0.306-0.2480.3930.11440.3968-0.01470.01160.17210.04630.282435.1244-40.109756.4346
105.96960.5386-1.37721.7103-0.48823.037-0.2825-0.1728-0.11330.02110.1218-0.16210.17310.24460.05820.21880.07410.04420.28860.00510.317-44.1902-31.58830.2293
110.20750.0436-0.1680.6697-0.63670.6492-0.1861-0.0591-0.0695-0.196-0.14080.043-0.0388-0.1223-0.41130.9432-0.3967-0.21451.2271-0.50091.2385-18.2893-40.472745.9662
120.6361-0.3235-0.60580.37741.84197.47080.098-0.3572-0.20120.0211-0.2150.12280.5745-0.97340.12720.604-0.11040.08020.7320.01730.395513.2796-40.750194.1706
135.49731.16912.30890.34081.02315.41260.3203-0.55370.09170.9353-0.1067-0.16710.4672-0.11-0.22391.00670.1227-0.11640.2987-0.07550.405422.3663-13.388672.8767
144.74640.2945-1.01186.20061.43.99250.10620.95950.1619-0.76520.1498-0.319-0.939-0.0367-0.15260.8168-0.0288-0.00021.15250.35780.799312.55725.0068-13.7639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 104 )A1 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 209 )A105 - 209
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 328 )A210 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 429 )A329 - 429
5X-RAY DIFFRACTION5chain 'A' and (resid 430 through 534 )A430 - 534
6X-RAY DIFFRACTION6chain 'A' and (resid 535 through 577 ) or chain 'B' and (resid 746 through 806 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 578 through 642 )A578 - 642
8X-RAY DIFFRACTION8chain 'B' and (resid 807 through 917 )B807 - 917
9X-RAY DIFFRACTION9chain 'B' and (resid 1334 through 1474 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 968 through 1265 )B968 - 1265
11X-RAY DIFFRACTION11chain 'B' and ((resid 918 through 967) or (resid 1266 through 1333))B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1475 through 1641 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 727 through 745 )B727 - 745
14X-RAY DIFFRACTION14chain 'C'C1 - 15

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