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- PDB-8hq1: Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 -

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Basic information

Entry
Database: PDB / ID: 8hq1
TitleCrystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2
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: 4.17 Å
AuthorsLiu, H.L. / Lin, Z.H. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270767 China
CitationJournal: To Be Published
Title: Structure Of Human Lgi1-Adam22 Complex In Space Group C2
Authors: Liu, H.L. / Lin, Z.H. / Xu, F.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
B: Disintegrin and metalloproteinase domain-containing protein 22
C: Disintegrin and metalloproteinase domain-containing protein 22
D: Leucine-rich glioma-inactivated protein 1
E: Leucine-rich glioma-inactivated protein 1
F: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,54236
Polymers343,0796
Non-polymers4,46330
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
3
C: Disintegrin and metalloproteinase domain-containing protein 22
F: 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)373.503, 232.369, 80.035
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number5
Space group name H-MC121

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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.: 3
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.: 3
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.: 18
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.: 12 / 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: 5.04 Å3/Da / Density % sol: 75.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 4.17→50 Å / Num. obs: 50134 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.04 / Net I/σ(I): 19.667
Reflection shellResolution: 4.17→4.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.909 / Num. unique obs: 4928 / Rsym value: 0.502 / % possible all: 98.1

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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: 4.17→37.92 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.68
RfactorNum. reflection% reflection
Rfree0.314 2557 5.11 %
Rwork0.266 --
obs0.268 49992 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.17→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23733 0 264 0 23997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424591
X-RAY DIFFRACTIONf_angle_d0.91933324
X-RAY DIFFRACTIONf_dihedral_angle_d18.6859231
X-RAY DIFFRACTIONf_chiral_restr0.0633690
X-RAY DIFFRACTIONf_plane_restr0.0044260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.172-4.25210.48251130.44852414X-RAY DIFFRACTION91
4.2521-4.33880.44611300.40712625X-RAY DIFFRACTION99
4.3388-4.4330.45271380.37162687X-RAY DIFFRACTION100
4.433-4.5360.45231110.34042645X-RAY DIFFRACTION100
4.536-4.64920.39161280.32132679X-RAY DIFFRACTION100
4.6492-4.77470.36341430.31422678X-RAY DIFFRACTION100
4.7747-4.91490.37431510.29832611X-RAY DIFFRACTION100
4.9149-5.07320.33671220.26862689X-RAY DIFFRACTION100
5.0732-5.2540.33251490.26822629X-RAY DIFFRACTION100
5.254-5.46380.30091700.27292631X-RAY DIFFRACTION100
5.4638-5.71170.35361670.27982655X-RAY DIFFRACTION100
5.7117-6.01170.3261420.27192622X-RAY DIFFRACTION100
6.0117-6.38670.34811410.27272647X-RAY DIFFRACTION100
6.3867-6.87710.31481500.26712659X-RAY DIFFRACTION100
6.8771-7.56420.3431530.26792632X-RAY DIFFRACTION100
7.5642-8.64750.29641510.25122648X-RAY DIFFRACTION99
8.6475-10.85240.2521710.22222632X-RAY DIFFRACTION99
10.8524-37.9170.26211270.22182652X-RAY DIFFRACTION97

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