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- PDB-8hpy: Crystal structure of human LGI1-ADAM22 complex -

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Basic information

Entry
Database: PDB / ID: 8hpy
TitleCrystal structure of human LGI1-ADAM22 complex
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 / axon guidance / central nervous system development / postsynaptic density membrane / 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 / axon guidance / central nervous system development / postsynaptic density membrane / metalloendopeptidase activity / integrin binding / neuron projection development / nervous system development / positive regulation of cell growth / cell adhesion / signaling receptor binding / axon / dendrite / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / 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. ...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. / EGF-like domain / Leucine-rich repeat / 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: 5.87 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 human LGI1-ADAM22 complex
Authors: Liu, H. / Xu, F.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)231,69524
Polymers228,7194
Non-polymers2,97520
Water00
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)115,84712
Polymers114,3602
Non-polymers1,48810
Water0
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)115,84712
Polymers114,3602
Non-polymers1,48810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)280.342, 280.342, 280.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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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: 60616.598 Da / Num. of mol.: 2
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: 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.: 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 5.87→50 Å / Num. obs: 9884 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.058 / Net I/σ(I): 25.905
Reflection shellResolution: 5.87→5.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.514 / Num. unique obs: 502 / Rsym value: 0.625 / % possible all: 100

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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: 5ZXR

5zxr
PDB Unreleased entry


Resolution: 5.87→48.08 Å / SU ML: 1.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.57
RfactorNum. reflection% reflection
Rfree0.343 491 5.04 %
Rwork0.303 --
obs0.305 9743 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.87→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15786 0 176 0 15962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416356
X-RAY DIFFRACTIONf_angle_d1.01222164
X-RAY DIFFRACTIONf_dihedral_angle_d14.5966142
X-RAY DIFFRACTIONf_chiral_restr0.062456
X-RAY DIFFRACTIONf_plane_restr0.0042832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.87-6.4550.52981200.41222302X-RAY DIFFRACTION99
6.455-7.38620.43111490.3812327X-RAY DIFFRACTION99
7.3862-9.29480.33961040.35542320X-RAY DIFFRACTION98
9.2948-48.07980.30061180.2562303X-RAY DIFFRACTION95

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