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- PDB-8hq2: Crystal structure of human ADAM22 in complex with human LGI1 mutant -

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Basic information

Entry
Database: PDB / ID: 8hq2
TitleCrystal structure of human ADAM22 in complex with human LGI1 mutant
Components
  • Disintegrin and metalloproteinase domain-containing protein 22
  • Leucine-rich glioma-inactivated protein 1
KeywordsMEMBRANE PROTEIN / SYNAPTIC MODULATOR / COMPLEX
Function / homology
Function and homology information


LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / myelination / central nervous system development / axon guidance / metalloendopeptidase activity ...LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / myelination / central nervous system development / axon guidance / metalloendopeptidase activity / neuron projection development / integrin binding / nervous system development / positive regulation of cell growth / cell adhesion / axon / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide ...Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / EGF-like domain, extracellular / EGF-like domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Metallopeptidase, catalytic domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / EGF-like domain signature 1. / Leucine-rich repeat / EGF-like domain / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich glioma-inactivated protein 1 / Disintegrin and metalloproteinase domain-containing protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLiu, H. / Lin, Z. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31270767 China
CitationJournal: To Be Published
Title: Crystal structure of human ADAM22 in complex with human LGI1 mutant
Authors: Liu, H. / Lin, Z. / 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

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Assembly

Deposited unit
A: Disintegrin and metalloproteinase domain-containing protein 22
D: Leucine-rich glioma-inactivated protein 1
B: Disintegrin and metalloproteinase domain-containing protein 22
E: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,48624
Polymers228,5114
Non-polymers2,97520
Water3,135174
1
A: Disintegrin and metalloproteinase domain-containing protein 22
D: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,74312
Polymers114,2552
Non-polymers1,48810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disintegrin and metalloproteinase domain-containing protein 22
E: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,74312
Polymers114,2552
Non-polymers1,48810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.250, 98.854, 131.258
Angle α, β, γ (deg.)96.21, 100.44, 91.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Disintegrin and metalloproteinase domain-containing protein 22 / ADAM 22 / Metalloproteinase-disintegrin ADAM22-3 / Metalloproteinase-like / disintegrin-like / and ...ADAM 22 / Metalloproteinase-disintegrin ADAM22-3 / Metalloproteinase-like / disintegrin-like / and cysteine-rich protein 2


Mass: 53743.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM22, MDC2 / Production host: Homo sapiens (human) / References: UniProt: Q9P0K1
#2: Protein Leucine-rich glioma-inactivated protein 1 / Epitempin-1


Mass: 60512.379 Da / Num. of mol.: 2 / Mutation: L88N/F89A/R474Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGI1, EPT, UNQ775/PRO1569 / Production host: Homo sapiens (human) / References: UniProt: O95970
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 54802 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.064 / Net I/σ(I): 21.167
Reflection shellResolution: 2.93→2.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 2.125 / Num. unique obs: 2716 / Rsym value: 0.694 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W8A, 5SXM, 3G5C

1w8a

5sxm

3g5c


Resolution: 2.93→45.83 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 34.93
RfactorNum. reflection% reflection
Rfree0.291 2702 4.95 %
Rwork0.245 --
obs0.247 54580 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.93→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15782 0 176 174 16132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416350
X-RAY DIFFRACTIONf_angle_d0.74822122
X-RAY DIFFRACTIONf_dihedral_angle_d17.6856138
X-RAY DIFFRACTIONf_chiral_restr0.052444
X-RAY DIFFRACTIONf_plane_restr0.0042822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9315-2.98480.42411000.33562388X-RAY DIFFRACTION84
2.9848-3.04220.35661380.31832663X-RAY DIFFRACTION98
3.0422-3.10430.3561510.30732786X-RAY DIFFRACTION98
3.1043-3.17180.3451490.29222758X-RAY DIFFRACTION98
3.1718-3.24550.36361430.30522718X-RAY DIFFRACTION98
3.2455-3.32670.3661430.29092820X-RAY DIFFRACTION98
3.3267-3.41660.34551350.28062720X-RAY DIFFRACTION98
3.4166-3.51710.3051600.26662752X-RAY DIFFRACTION98
3.5171-3.63060.32451420.2632742X-RAY DIFFRACTION99
3.6306-3.76030.28621350.26622801X-RAY DIFFRACTION98
3.7603-3.91080.321370.2622736X-RAY DIFFRACTION98
3.9108-4.08860.29071490.23782812X-RAY DIFFRACTION99
4.0886-4.3040.261380.22622732X-RAY DIFFRACTION99
4.304-4.57350.24491420.21362778X-RAY DIFFRACTION99
4.5735-4.92620.26421550.21262782X-RAY DIFFRACTION99
4.9262-5.42130.22841330.21912751X-RAY DIFFRACTION98
5.4213-6.20410.34521310.2482780X-RAY DIFFRACTION98
6.2041-7.81020.28331510.26482733X-RAY DIFFRACTION98
7.8102-45.830.2661700.20572626X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -17.3372 Å / Origin y: -59.4042 Å / Origin z: -63.7304 Å
111213212223313233
T0.3182 Å2-0.0598 Å20.0104 Å2-0.5399 Å2-0.0826 Å2--0.525 Å2
L0.2591 °20.0737 °2-0.0574 °2-0.7998 °2-0.1774 °2--0.3839 °2
S-0.0095 Å °-0.0485 Å °-0.0099 Å °0.0598 Å °-0.0645 Å °-0.1095 Å °-0.03 Å °-0.0578 Å °0.0594 Å °
Refinement TLS groupSelection details: ALL

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