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- PDB-8hpw: Crystal structure of mouse LGI1 LRR domain in space group P21 -

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Basic information

Entry
Database: PDB / ID: 8hpw
TitleCrystal structure of mouse LGI1 LRR domain in space group P21
ComponentsLeucine-rich glioma-inactivated protein 1
KeywordsSIGNALING PROTEIN / Synaptic modulator / LRR domain
Function / homology
Function and homology information


LGI-ADAM interactions / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / neuron projection development / positive regulation of cell growth / signaling receptor binding / glutamatergic synapse ...LGI-ADAM interactions / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / neuron projection development / positive regulation of cell growth / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / extracellular space / cytoplasm
Similarity search - Function
Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich glioma-inactivated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLiu, H. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270767 China
CitationJournal: To Be Published
Title: Crystal structure of mouse LGI1 LRR domain in space group P21
Authors: Liu, H. / Xu, F.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich glioma-inactivated protein 1
B: Leucine-rich glioma-inactivated protein 1
C: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4486
Polymers68,7843
Non-polymers6643
Water2,234124
1
A: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers22,9281
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers22,9281
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers22,9281
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.158, 101.694, 65.848
Angle α, β, γ (deg.)90.00, 91.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leucine-rich glioma-inactivated protein 1


Mass: 22928.094 Da / Num. of mol.: 3 / Fragment: LRR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgi1 / Production host: Homo sapiens (human) / References: UniProt: Q9JIA1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.64 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 18% PEG 3000, 0.1M potassium/sodium phosphate pH=6.2, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 28150 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.076 / Net I/σ(I): 20.383
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.271 / Num. unique obs: 1416 / Rsym value: 0.242 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W8A

1w8a


Resolution: 2.39→40.24 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.02
RfactorNum. reflection% reflection
Rfree0.246 1388 4.98 %
Rwork0.22 --
obs0.221 27856 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.39→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 42 124 4447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034463
X-RAY DIFFRACTIONf_angle_d0.8416075
X-RAY DIFFRACTIONf_dihedral_angle_d16.1091684
X-RAY DIFFRACTIONf_chiral_restr0.064697
X-RAY DIFFRACTIONf_plane_restr0.005781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.47210.37051490.32412590X-RAY DIFFRACTION96
2.4721-2.57110.37371350.30242606X-RAY DIFFRACTION98
2.5711-2.68810.31311230.29372667X-RAY DIFFRACTION98
2.6881-2.82980.31791280.28952648X-RAY DIFFRACTION98
2.8298-3.0070.32651260.29332690X-RAY DIFFRACTION99
3.007-3.23910.26591660.27072615X-RAY DIFFRACTION99
3.2391-3.56490.26111290.2382694X-RAY DIFFRACTION99
3.5649-4.08030.2021680.19932655X-RAY DIFFRACTION99
4.0803-5.1390.20821430.17462705X-RAY DIFFRACTION100
5.139-40.240.22821210.18742598X-RAY DIFFRACTION94
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)
19.93670.3435-1.97918.30231.46259.2938-0.160.10390.0175-0.34570.1036-1.0456-0.04131.82940.02040.6511-0.07770.01021.1526-0.01390.634376.1857-12.9685142.6507
25.026-1.6464-1.29151.79550.44116.1610.04790.28910.3903-0.21650.0317-0.2087-0.14850.4692-0.07750.5602-0.1252-0.02090.56620.03610.38360.7765-9.7542142.8188
32.9058-2.8261-1.16784.2711-0.89853.21730.1263-0.2365-0.2813-0.07560.01490.639-0.0045-0.4662-0.11550.6015-0.161-0.02890.79980.05870.626245.6784-9.8414147.6976
48.2908-4.10232.74167.1895-2.66694.572-0.5804-1.140.08050.59180.73240.441-0.6422-2.0495-0.20450.74420.02620.16161.38240.04870.554640.1273-4.0453154.9053
55.1119-0.7196-0.98435.5385-1.1724.08870.01360.0340.1323-0.4475-0.0718-0.0397-0.954-0.07230.05920.7124-0.0962-0.01830.84040.04570.373160.7629-14.122118.5524
61.87771.01130.6447.85510.47743.61740.03150.0905-0.33170.83880.1446-0.0590.67890.172-0.15790.8174-0.0395-0.01340.7977-0.05660.476565.5165-34.7833126.6711
76.02521.41823.42687.5812.10472.23340.41280.4922-1.2846-1.665-0.23681.33331.091-0.3601-0.08681.1155-0.0348-0.07091.0547-0.06010.639164.6897-25.4855100.1097
82.22291.8527-0.45939.5916-0.01028.3-0.06780.7513-0.7169-0.4582-0.385-0.55242.2712-0.25540.33060.8157-0.00660.00720.750.03180.502468.4828-22.336294.8989
94.05910.69960.23454.3099-0.10276.8097-0.10960.1247-0.0772-0.06440.0021-0.33750.03761.46630.12330.65240.05090.02710.99930.02090.435676.6571-13.632799.3954
103.40190.2316-1.30546.0458-1.20528.06420.0437-0.9324-0.0704-0.0326-0.229-0.2426-0.65531.92580.17860.7969-0.34530.03471.3312-0.07450.539482.255-5.0983105.6141
112.63250.59640.87285.8341-1.48392.50540.5914-0.9890.11320.6179-0.2889-0.7722-1.60532.4198-0.1751.2909-0.56130.00092.1131-0.08720.756789.296-1.1398109.1508
129.17610.67660.82423.95730.42064.07070.5435-0.95510.91550.50370.3131-1.0303-1.7892.1771-0.77081.5353-0.65580.00092.4174-0.33750.994891.65950.3539115.4162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 41 THROUGH 70 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 71 THROUGH 155 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 156 THROUGH 190 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 191 THROUGH 221 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 41 THROUGH 90 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 91 THROUGH 221 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 41 THROUGH 56 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 57 THROUGH 70 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 71 THROUGH 145 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 146 THROUGH 169 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 170 THROUGH 190 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 191 THROUGH 221 )

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