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- PDB-7lu6: Crystal structure of the mouse Kirrel3 D1 homodimer -

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Basic information

Entry
Database: PDB / ID: 7lu6
TitleCrystal structure of the mouse Kirrel3 D1 homodimer
ComponentsKin of IRRE-like protein 3
KeywordsCELL ADHESION / Immunoglobulin superfamily / Cell surface receptor / Nervous system
Function / homology
Function and homology information


inter-male aggressive behavior / Nephrin family interactions / glomerulus morphogenesis / principal sensory nucleus of trigeminal nerve development / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / hemopoiesis / cell adhesion molecule binding / synapse assembly / neuron projection morphogenesis ...inter-male aggressive behavior / Nephrin family interactions / glomerulus morphogenesis / principal sensory nucleus of trigeminal nerve development / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / hemopoiesis / cell adhesion molecule binding / synapse assembly / neuron projection morphogenesis / dendritic shaft / PDZ domain binding / hippocampus development / neuron migration / cell-cell adhesion / cell-cell junction / synaptic vesicle / membrane => GO:0016020 / axon / dendrite / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Kin of IRRE-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRoman, C.A. / Pak, J.S. / Wang, J. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Cell Rep / Year: 2021
Title: Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors.
Authors: Wang, J. / Vaddadi, N. / Pak, J.S. / Park, Y. / Quilez, S. / Roman, C.A. / Dumontier, E. / Thornton, J.W. / Cloutier, J.F. / Ozkan, E.
History
DepositionFeb 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Kin of IRRE-like protein 3
B: Kin of IRRE-like protein 3
C: Kin of IRRE-like protein 3
D: Kin of IRRE-like protein 3
E: Kin of IRRE-like protein 3
F: Kin of IRRE-like protein 3
G: Kin of IRRE-like protein 3
H: Kin of IRRE-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42216
Polymers97,2388
Non-polymers1848
Water6,053336
1
A: Kin of IRRE-like protein 3
B: Kin of IRRE-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3554
Polymers24,3092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-26 kcal/mol
Surface area10240 Å2
MethodPISA
2
C: Kin of IRRE-like protein 3
D: Kin of IRRE-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3554
Polymers24,3092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-31 kcal/mol
Surface area10180 Å2
MethodPISA
3
E: Kin of IRRE-like protein 3
F: Kin of IRRE-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3554
Polymers24,3092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-33 kcal/mol
Surface area10260 Å2
MethodPISA
4
G: Kin of IRRE-like protein 3
H: Kin of IRRE-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3554
Polymers24,3092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-33 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.241, 63.241, 347.809
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein
Kin of IRRE-like protein 3 / Kin of irregular chiasm-like protein 3 / Nephrin-like protein 2 / mKirre


Mass: 12154.733 Da / Num. of mol.: 8 / Fragment: Domain 1, residues 47-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kirrel3, Kiaa1867, Neph2 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8BR86
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium cacodylate, pH 6.5, 1.4 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2015
RadiationMonochromator: Single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 57041 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.062 / Rrim(I) all: 0.13 / Rsym value: 0.114 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2865 / CC1/2: 0.617 / CC star: 0.874 / Rpim(I) all: 0.459 / Rrim(I) all: 0.97 / Rsym value: 0.853 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot0.9.3model building
PHASER2.6.0phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LTW

7ltw


Resolution: 1.95→49.52 Å / Cross valid method: FREE R-VALUE / Phase error: 26.9666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 2846 4.99 %
Rwork0.1602 54138 -
obs0.1648 56984 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6246 0 8 336 6590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00466572
X-RAY DIFFRACTIONf_angle_d0.68419007
X-RAY DIFFRACTIONf_chiral_restr0.05031029
X-RAY DIFFRACTIONf_plane_restr0.00521186
X-RAY DIFFRACTIONf_dihedral_angle_d13.42792423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.27481130.22952691X-RAY DIFFRACTION93.63
1.98-2.020.24371650.21282647X-RAY DIFFRACTION94
2.02-2.060.23861490.2122709X-RAY DIFFRACTION94.59
2.06-2.10.24791670.20252696X-RAY DIFFRACTION94.07
2.1-2.150.22541550.19222675X-RAY DIFFRACTION94.49
2.15-2.20.18281360.19012718X-RAY DIFFRACTION95.17
2.2-2.250.21531220.18782715X-RAY DIFFRACTION95.63
2.25-2.310.20731520.19032688X-RAY DIFFRACTION94.58
2.31-2.380.19621700.18432691X-RAY DIFFRACTION93.99
2.38-2.460.25631320.17122710X-RAY DIFFRACTION95.29
2.46-2.540.23111360.17582733X-RAY DIFFRACTION95.26
2.54-2.640.19461300.17442725X-RAY DIFFRACTION95.45
2.65-2.770.19861800.16882654X-RAY DIFFRACTION93.65
2.77-2.910.21281140.17152739X-RAY DIFFRACTION96
2.91-3.090.18861590.16022689X-RAY DIFFRACTION94.42
3.09-3.330.2191210.15622772X-RAY DIFFRACTION95.78
3.33-3.670.14821360.1412705X-RAY DIFFRACTION95.21
3.67-4.20.1491370.13332737X-RAY DIFFRACTION95.2
4.2-5.290.18431390.11992711X-RAY DIFFRACTION95.02
5.29-49.520.19681330.17062733X-RAY DIFFRACTION94.93
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)
11.872617392-0.0158505556863-0.8242824259111.728179126080.3225574214911.91929535832-0.005505508203010.199632824371-0.093699802178-0.1359557224860.0339916692897-0.01738052130980.138624156608-0.0129745379942-0.03120811539520.190446271066-0.00773223555808-0.03107369981760.131115449554-0.01409131056350.06910234286682.2855416174718.7022751116-47.8207131443
22.41416910783-0.206477426869-0.9107279521341.23167303972-0.3682784707873.11548707137-0.0502218662699-0.289846609794-0.1184288412490.1967882252110.07332571239310.01717319880170.363247303298-0.0576501914577-0.01943990251480.284714607303-0.00834380958534-0.02202124646490.1758942846850.01828279514470.079585934516-3.1552281363318.8946356561-24.4409586907
33.151150137990.206709679657-0.248057579791.546046653270.2710621622172.912595653760.02908934802160.341659601861-0.0374039293228-0.1861118672540.00473609013973-0.1046362521520.3316145526080.207133350861-0.0206011534230.2611413356460.01496189195030.02627674449020.186614112222-0.00536633862340.08972206234346.8394002811217.7940203182-91.5244655298
42.16920858731-0.6899183057670.6028369042471.52858947994-0.1273566477742.372292261680.0995829810744-0.0237363261772-0.0172745816781-0.01432452272030.007220220480110.03024188496140.142572112243-0.0568299616342-0.08602191674370.190425469622-0.01873857267930.007718899053690.1293558083250.006264470358950.06509556285271.5086793535418.9344444648-68.1470421827
55.088117484380.0778801389911-1.718627178622.02747747796-0.5022962995042.7504700958-0.289253440412-0.154573011030.1329396997250.03254245696350.2730899481960.09204967649980.278380263366-0.3198769103850.04740519117120.5126764718050.0285800169581-0.03040163019290.52542034099-0.01041957379910.155242259787-1.1798157858117.7016995312-4.26842006912
63.767041360251.23794638824-2.40044061572.16226151864-1.082533358285.90544047905-0.0260863799312-0.1953763781170.1717756101690.2195000465890.1543983997640.0898081509272-0.03515864385180.200053805521-0.08314617327950.7250910902560.0926123896540.03268863414810.7604357581570.04528247449790.218449097737-7.5411382128816.084405219519.1097478598
74.099095700650.275456895778-4.571026500722.76740471331-0.8989126902915.564314767430.003996075615340.1315674941710.201452451091-0.3179163660730.276005591693-0.0598992796247-0.2103453846660.105130786142-0.301356482240.686469487879-0.001275411072380.02191162924150.78502878771-0.05251044568110.234943587749-5.9839669498116.93735254239.0135932159
83.974423839061.37578526441-2.483471620164.70539004655-0.5548864115568.693885148550.309115356359-0.265421386570.133243102465-0.2006090570950.1452400830480.0263954245209-0.3337523338991.14013168206-0.3231729625740.471842909878-0.03564070245020.03465091834620.760811391586-0.05152442303070.148059409299-12.237202010513.535962579562.1413175793
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain AAA - B45 - 1001
22chain BBC - D46 - 1001
33chain CCE - F45 - 1001
44chain DDG - H47 - 1001
55chain EEI - J47 - 1001
66chain FFK - L47 - 1001
77chain GGM - N47 - 1001
88chain HHO - P48 - 1001

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