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- PDB-8axj: Crystal structure of the N-terminal domain of Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 8axj
TitleCrystal structure of the N-terminal domain of Trypanosoma brucei CFAP410
ComponentsChains: A
KeywordsSTRUCTURAL PROTEIN / Cilia / Flagella / Leucine rich repeat
Function / homology
Function and homology information


: / CFAP410 C-terminal domain / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / CFAP410 C-terminal domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsDong, G. / Stadler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI5960-B2 Austria
CitationJournal: Front Cell Dev Biol / Year: 2025
Title: CFAP410 has a bimodular architecture with a conserved surface patch on its N-terminal leucine-rich repeat motif for binding interaction partners.
Authors: Stadler, A. / Gabriel, H.B. / De Liz, L.V. / Alonso-Gil, S. / Deng, X. / Crickley, R. / Korbula, K. / Mikolaskova, B. / Vaughan, S. / Huang, K. / Zagrovic, B. / Sunter, J.D. / Dong, G.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.2Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,02110
Polymers18,1861
Non-polymers8359
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-15 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.799, 52.960, 61.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chains: A


Mass: 18185.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38DI2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.1 M sodium citrate, 1 M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1→19.9 Å / Num. obs: 69889 / % possible obs: 98.17 % / Redundancy: 11.4 % / Biso Wilson estimate: 10.25 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 10.84
Reflection shellResolution: 1→1.04 Å / Num. unique obs: 5835 / CC1/2: 0.386 / % possible all: 83.75

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4P

6l4p


Resolution: 1→19.9 Å / SU ML: 0.112 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1623 1999 2.86 %
Rwork0.1508 67890 -
obs0.1512 69889 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.15 Å2
Refinement stepCycle: LAST / Resolution: 1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 52 157 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021372
X-RAY DIFFRACTIONf_angle_d1.2211869
X-RAY DIFFRACTIONf_chiral_restr0.0885221
X-RAY DIFFRACTIONf_plane_restr0.009241
X-RAY DIFFRACTIONf_dihedral_angle_d15.3504208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.40931050.4043565X-RAY DIFFRACTION72.56
1.02-1.050.32741340.324549X-RAY DIFFRACTION92.73
1.05-1.080.25351430.254866X-RAY DIFFRACTION99.07
1.08-1.110.21951450.18774913X-RAY DIFFRACTION99.94
1.11-1.150.18631460.174923X-RAY DIFFRACTION99.96
1.15-1.20.17051450.14054932X-RAY DIFFRACTION99.96
1.2-1.250.15661450.12844946X-RAY DIFFRACTION99.98
1.25-1.320.1521450.12864938X-RAY DIFFRACTION100
1.32-1.40.16721460.12424955X-RAY DIFFRACTION99.98
1.4-1.510.14141470.11944968X-RAY DIFFRACTION100
1.51-1.660.14321470.11885002X-RAY DIFFRACTION100
1.66-1.90.14241470.1265002X-RAY DIFFRACTION100
1.9-2.40.13381490.135072X-RAY DIFFRACTION100
2.4-19.90.16241550.16155259X-RAY DIFFRACTION99.96

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