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- PDB-6xz6: Structure of the trypanosome brucei factor H receptor bound to do... -

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Basic information

Entry
Database: PDB / ID: 6xz6
TitleStructure of the trypanosome brucei factor H receptor bound to domain D5 of bovine factor H
Components
  • Complement factor HFactor H
  • GARP domain-containing protein
KeywordsIMMUNE SYSTEM / Trypanosome brucei / immunity / complement system / factor H / factor H receptor
Function / homology
Function and homology information


complement activation, alternative pathway / post-transcriptional regulation of gene expression / extracellular region
Similarity search - Function
Trypanosoma glutamic acid/alanine-rich protein / Glutamic acid/alanine-rich protein of Trypanosoma / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile.
Similarity search - Domain/homology
Complement factor H / GARP domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMacleod, O.J.S. / Carrington, M. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P001424/1
CitationJournal: Nat Commun / Year: 2020
Title: A receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies.
Authors: Macleod, O.J.S. / Bart, J.M. / MacGregor, P. / Peacock, L. / Savill, N.J. / Hester, S. / Ravel, S. / Sunter, J.D. / Trevor, C. / Rust, S. / Vaughan, T.J. / Minter, R. / Mohammed, S. / ...Authors: Macleod, O.J.S. / Bart, J.M. / MacGregor, P. / Peacock, L. / Savill, N.J. / Hester, S. / Ravel, S. / Sunter, J.D. / Trevor, C. / Rust, S. / Vaughan, T.J. / Minter, R. / Mohammed, S. / Gibson, W. / Taylor, M.C. / Higgins, M.K. / Carrington, M.
History
DepositionFeb 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GARP domain-containing protein
B: Complement factor H
C: GARP domain-containing protein
D: Complement factor H


Theoretical massNumber of molelcules
Total (without water)63,5724
Polymers63,5724
Non-polymers00
Water3,333185
1
A: GARP domain-containing protein
B: Complement factor H


Theoretical massNumber of molelcules
Total (without water)31,7862
Polymers31,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-4 kcal/mol
Surface area14630 Å2
MethodPISA
2
C: GARP domain-containing protein
D: Complement factor H


Theoretical massNumber of molelcules
Total (without water)31,7862
Polymers31,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-6 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.505, 66.056, 71.018
Angle α, β, γ (deg.)90.000, 94.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GARP domain-containing protein


Mass: 24771.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.5.4020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57Z47
#2: Protein Complement factor H / Factor H / H factor 1


Mass: 7015.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CFH, HF1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q28085
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 17 % (w/v) polyethylene glycol 10,000, 0.1 M Bis-(2-hydroxyethyl)imino-tris(hydroxymethyl)methane, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→27.77 Å / Num. obs: 20315 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.978 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1049 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4O

4e4o


Resolution: 2.7→27.77 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / SU R Cruickshank DPI: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.668 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1049 5.16 %RANDOM
Rwork0.192 ---
obs0.195 20315 98.9 %-
Displacement parametersBiso max: 170.83 Å2 / Biso mean: 43.81 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1--6.3289 Å20 Å2-8.0828 Å2
2--1.8028 Å20 Å2
3---4.5261 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.7→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 0 185 4371
Biso mean---37.26 -
Num. residues----544
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1540SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes754HARMONIC5
X-RAY DIFFRACTIONt_it4244HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion556SEMIHARMONIC5
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_contact4746SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d4244HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5718HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion21.4
LS refinement shellResolution: 2.7→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3377 25 6.14 %
Rwork0.2298 382 -
all0.2357 407 -
obs--98.13 %
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)
11.5990.65640.3510.01510.51740.43630.1707-0.18130.28280.092-0.11580.13630.2222-0.0043-0.0550.0064-0.01930.051-0.10330.02030.0095-16.7647-4.3778-0.6545
20.7430.64060.53292.0166-0.1132.426-0.01330.31280.0216-0.0358-0.09150.0526-0.1422-0.24460.1049-0.01620.0015-0.0119-0.04850.0454-0.0644-37.4309-12.3249-31.7654
3-0.0222-0.23030.12051.2199-0.64150.5688-0.0998-0.03490.0514-0.26420.0304-0.21420.1784-0.10320.06940.05020.02580.1015-0.13210.062-0.0166-23.8432-1.287512.7342
41.2480.1858-0.28760.33030.3581.605-0.0708-0.1430.1270.00440.0344-0.03940.22480.41050.03640.0440.09220.0561-0.05950.1134-0.0982-19.5979-25.031142.1148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A25 - 237
2X-RAY DIFFRACTION2{ B|* }B264 - 322
3X-RAY DIFFRACTION3{ C|* }C25 - 237
4X-RAY DIFFRACTION4{ D|* }D264 - 322

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