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- PDB-8axr: Crystal structure of the C-terminal domain of human CFAP410 -

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Basic information

Entry
Database: PDB / ID: 8axr
TitleCrystal structure of the C-terminal domain of human CFAP410
ComponentsCilia- and flagella-associated protein 410
KeywordsSTRUCTURAL PROTEIN / Cilia / Flagella / Coiled-coil
Function / homology
Function and homology information


photoreceptor connecting cilium / smoothened signaling pathway / cilium assembly / photoreceptor outer segment / cytoskeleton organization / ciliary basal body / regulation of cell shape / intracellular membrane-bounded organelle / DNA damage response / mitochondrion ...photoreceptor connecting cilium / smoothened signaling pathway / cilium assembly / photoreceptor outer segment / cytoskeleton organization / ciliary basal body / regulation of cell shape / intracellular membrane-bounded organelle / DNA damage response / mitochondrion / plasma membrane / cytosol / cytoplasm
Similarity search - Function
U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Cilia- and flagella-associated protein 410
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsDong, G. / Stadler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI5960-B2 Austria
CitationJournal: To Be Published
Title: Structural studies of cilia and flagella associated protein 410 (CFAP410) reveal its bimodular organization with an N-terminal LRR motif and a C-terminal tetrameric helical bundle
Authors: Dong, G. / Stadler, A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cilia- and flagella-associated protein 410
B: Cilia- and flagella-associated protein 410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1734
Polymers7,1022
Non-polymers712
Water50428
1
A: Cilia- and flagella-associated protein 410
B: Cilia- and flagella-associated protein 410
hetero molecules

A: Cilia- and flagella-associated protein 410
B: Cilia- and flagella-associated protein 410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3468
Polymers14,2044
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6150 Å2
ΔGint-95 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.115, 50.628, 22.146
Angle α, β, γ (deg.)90.000, 101.079, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide Cilia- and flagella-associated protein 410 / C21orf-HUMF09G8.5 / Leucine-rich repeat-containing protein 76 / YF5/A2


Mass: 3551.079 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFAP410, C21orf2, LRRC76 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43822
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 297 K / Method: evaporation / Details: 1.5 M sodium chloride, 10% (v/v) ethanol / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.5→19.94 Å / Num. obs: 9761 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.0335 / Rrim(I) all: 0.084 / Net I/σ(I): 11.05
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 948 / CC1/2: 0.519 / CC star: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
xia2data reduction
xia2data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→19.94 Å / SU ML: 0.2313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 977 10.01 %
Rwork0.2106 8779 -
obs0.2139 9756 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 2 28 482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063450
X-RAY DIFFRACTIONf_angle_d0.9367609
X-RAY DIFFRACTIONf_chiral_restr0.073484
X-RAY DIFFRACTIONf_plane_restr0.009577
X-RAY DIFFRACTIONf_dihedral_angle_d4.521962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.37011350.33691210X-RAY DIFFRACTION95.66
1.58-1.680.32461370.28641231X-RAY DIFFRACTION99.85
1.68-1.80.29741400.25721255X-RAY DIFFRACTION99.86
1.8-1.990.26521390.23331264X-RAY DIFFRACTION99.72
1.99-2.270.25031410.20291258X-RAY DIFFRACTION99.86
2.27-2.860.22851400.20651269X-RAY DIFFRACTION100
2.86-19.940.22021450.19181292X-RAY DIFFRACTION99.52
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)
10.1350097960920.03897271266210.06552071150030.05868647018640.05682240496830.0593429392429-0.06307877008110.03026326763490.1703329892840.308815240411-0.0203105222882-0.122447652227-0.02829897085860.31757472949-0.0003737562099330.2845679176280.00461431774377-0.03181114639510.235416206998-0.01354260949170.2365461500998.644400088879.260432831576.66983922003
20.0928381041253-0.009800009739880.1033055257540.0823977276735-0.01780089608330.2142837225220.0655185506218-0.252389536321-0.0672623342494-0.084479080149-0.0315457987995-0.1493493721470.1455696407390.09155272250560.01167869799010.2085724535950.01742591880210.01390450435840.250625988311-0.0004817256917640.2411559272898.472874862256.317281327455.72978356237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 214 through 244)AA214 - 2441 - 31
22(chain 'B' and resid 214 through 242)BC214 - 2421 - 29

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