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- PDB-7pi6: Trypanosoma brucei ISG65 bound to human complement C3d -

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Basic information

Entry
Database: PDB / ID: 7pi6
TitleTrypanosoma brucei ISG65 bound to human complement C3d
Components
  • 65 kDa invariant surface glycoprotein
  • Complement C3dg fragment
KeywordsIMMUNE SYSTEM / Complement / innate immunity / host-pathogen / sleeping sickness
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 / plasma membrane organization / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / 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 / plasma membrane organization / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / 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 / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / 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) / azurophil granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / G alpha (i) signalling events / secretory granule lumen / blood microparticle / membrane => GO:0016020 / immune response / inflammatory response / positive regulation of protein phosphorylation / 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
Trypanosome invariant surface glycoprotein / Invariant surface glycoprotein / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 ...Trypanosome invariant surface glycoprotein / Invariant surface glycoprotein / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / 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/fibulin / Anaphylatoxin, complement system / 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
Complement C3 / 65 kDa invariant surface glycoprotein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCook, A.D. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Invariant surface glycoprotein 65 of Trypanosoma brucei is a complement C3 receptor.
Authors: Macleod, O.J.S. / Cook, A.D. / Webb, H. / Crow, M. / Burns, R. / Redpath, M. / Seisenberger, S. / Trevor, C.E. / Peacock, L. / Schwede, A. / Kimblin, N. / Francisco, A.F. / Pepperl, J. / ...Authors: Macleod, O.J.S. / Cook, A.D. / Webb, H. / Crow, M. / Burns, R. / Redpath, M. / Seisenberger, S. / Trevor, C.E. / Peacock, L. / Schwede, A. / Kimblin, N. / Francisco, A.F. / Pepperl, J. / Rust, S. / Voorheis, P. / Gibson, W. / Taylor, M.C. / Higgins, M.K. / Carrington, M.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 65 kDa invariant surface glycoprotein
B: Complement C3dg fragment
C: 65 kDa invariant surface glycoprotein
D: Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,74310
Polymers154,1634
Non-polymers5816
Water1,08160
1
A: 65 kDa invariant surface glycoprotein
B: Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3585
Polymers77,0812
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 65 kDa invariant surface glycoprotein
D: Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3865
Polymers77,0812
Non-polymers3043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.947, 189.578, 73.880
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 65 kDa invariant surface glycoprotein


Mass: 44369.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.2.3270 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q587F5
#2: Protein Complement C3dg fragment


Mass: 32711.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01024
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6, 0.2 M MgCl2, 20% PEG 6000 with sliver bullet HR2-996-55

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.6→94.79 Å / Num. obs: 43218 / % possible obs: 98.7 % / Redundancy: 2.9 % / CC1/2: 0.875 / Net I/σ(I): 3.6
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 4392 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3D

1c3d


Resolution: 2.6→94.79 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.766 / SU R Cruickshank DPI: 0.585 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.523 / SU Rfree Blow DPI: 0.332 / SU Rfree Cruickshank DPI: 0.347
RfactorNum. reflection% reflectionSelection details
Rfree0.31 2065 4.79 %RANDOM
Rwork0.2677 ---
obs0.2698 43143 98.6 %-
Displacement parametersBiso max: 104.22 Å2 / Biso mean: 51.08 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-11.6912 Å20 Å2-5.6724 Å2
2---26.9724 Å20 Å2
3---15.2812 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 2.6→94.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7859 0 38 60 7957
Biso mean--58.54 34.09 -
Num. residues----996
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2862SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1365HARMONIC5
X-RAY DIFFRACTIONt_it8039HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1019SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5928SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8039HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg10832HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion18.44
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3841 49 5.68 %
Rwork0.363 814 -
all0.3642 863 -
obs--95.55 %
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)
11.9708-3.17330.47975.0846-0.28670.44470.14570.1713-0.0966-0.1502-0.16030.0736-0.0012-0.07510.0146-0.21390.0070.0433-0.34190.0506-0.2586-25.752196.162837.7472
22.421-0.12060.09451.91890.3981.389-0.0362-0.09650.1509-0.0596-0.03060.0262-0.077-0.00460.0668-0.3365-0.00890.0477-0.3251-0.0153-0.2444-1.7304102.95556.8582
31.3242-2.1013-0.24253.5378-0.0581.00950.05090.22570.090.0506-0.02490.04820.15350.1365-0.0259-0.1840.0280.0276-0.2706-0.0522-0.345413.788569.97371.722
42.1997-0.1493-0.59881.2667-0.41361.5573-0.0192-0.0445-0.1158-0.128-0.06290.01940.0588-0.00320.0821-0.3476-0.00590.019-0.36060.0101-0.1744-7.261360.22619.8798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A27 - 316
2X-RAY DIFFRACTION2{ B|* }B996 - 1285
3X-RAY DIFFRACTION3{ C|* }C38 - 316
4X-RAY DIFFRACTION4{ D|* }D997 - 1285

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