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- PDB-8esf: Crystal structure of human Nischarin PX and LRR domains with engi... -

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Basic information

Entry
Database: PDB / ID: 8esf
TitleCrystal structure of human Nischarin PX and LRR domains with engineered mutations
ComponentsNischarin
KeywordsENDOCYTOSIS / Nischarin / PX domain / leucine-rich repeat domain
Function / homology
Function and homology information


RND2 GTPase cycle / RND3 GTPase cycle / Rac protein signal transduction / intercellular bridge / RAC1 GTPase cycle / phosphatidylinositol binding / negative regulation of cell migration / recycling endosome / integrin binding / microtubule cytoskeleton ...RND2 GTPase cycle / RND3 GTPase cycle / Rac protein signal transduction / intercellular bridge / RAC1 GTPase cycle / phosphatidylinositol binding / negative regulation of cell migration / recycling endosome / integrin binding / microtubule cytoskeleton / actin cytoskeleton organization / early endosome / intracellular membrane-bounded organelle / apoptotic process / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nischarin, PX domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / Nischarin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsEldershaw, D.E. / Collins, B.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: To Be Published
Title: Crystal structure of human Nischarin PX and LRR domains with engineered mutations
Authors: Eldershaw, D.E. / Collins, B.M.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nischarin
B: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8553
Polymers112,7862
Non-polymers691
Water50428
1
A: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4622
Polymers56,3931
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nischarin


Theoretical massNumber of molelcules
Total (without water)56,3931
Polymers56,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.173, 83.307, 90.830
Angle α, β, γ (deg.)90.000, 94.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Nischarin / Imidazoline receptor 1 / I-1 / IR1 / Imidazoline receptor antisera-selected protein / hIRAS / ...Imidazoline receptor 1 / I-1 / IR1 / Imidazoline receptor antisera-selected protein / hIRAS / Imidazoline-1 receptor / I1R / Imidazoline-1 receptor candidate protein / I-1 receptor candidate protein / I1R candidate protein


Mass: 56393.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NISCH, IRAS, KIAA0975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2I1
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole, 10% PEG-8000, 0.1 M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.56→49.12 Å / Num. obs: 42220 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 69.77 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 11.3
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 4092 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 2.56→43.96 Å / SU ML: 0.3487 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 2009 4.77 %
Rwork0.2153 40142 -
obs0.2167 42151 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.8 Å2
Refinement stepCycle: LAST / Resolution: 2.56→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6775 0 5 28 6808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01026910
X-RAY DIFFRACTIONf_angle_d1.34859366
X-RAY DIFFRACTIONf_chiral_restr0.0691105
X-RAY DIFFRACTIONf_plane_restr0.00981184
X-RAY DIFFRACTIONf_dihedral_angle_d13.68562575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.42931200.35962533X-RAY DIFFRACTION86.96
2.62-2.690.30471380.3032909X-RAY DIFFRACTION99.97
2.69-2.770.31651570.27212842X-RAY DIFFRACTION100
2.77-2.860.32831380.27762892X-RAY DIFFRACTION100
2.86-2.960.30831430.27332851X-RAY DIFFRACTION100
2.96-3.080.33841490.3052875X-RAY DIFFRACTION99.8
3.08-3.220.34721420.28152888X-RAY DIFFRACTION100
3.22-3.390.25321620.24122885X-RAY DIFFRACTION99.97
3.39-3.610.26591350.23312880X-RAY DIFFRACTION99.97
3.61-3.880.27821510.21882877X-RAY DIFFRACTION99.93
3.88-4.270.22331390.18732900X-RAY DIFFRACTION99.9
4.27-4.890.18251470.17772927X-RAY DIFFRACTION99.97
4.89-6.160.20311450.18992909X-RAY DIFFRACTION99.87
6.16-43.960.21051430.18832974X-RAY DIFFRACTION99.33

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