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- PDB-8y6b: Structure of human LGI1-ADAM22 complex in space group P212121 -

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Basic information

Entry
Database: PDB / ID: 8y6b
TitleStructure of human LGI1-ADAM22 complex in space group P212121
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: 3.49 Å
AuthorsLiu, H. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31270767 China
CitationJournal: To Be Published
Title: Structure of human LGI1-ADAM22 complex in space group P212121
Authors: Liu, H. / Xu, F.
History
DepositionFeb 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
C: Disintegrin and metalloproteinase domain-containing protein 22
F: Leucine-rich glioma-inactivated protein 1
E: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,54236
Polymers343,0796
Non-polymers4,46330
Water3,531196
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.448, 196.078, 420.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.

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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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 58327 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.064 / Rsym value: 0.063 / Net I/σ(I): 14.582
Reflection shellResolution: 3.49→3.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.806 / Num. unique obs: 2737 / Rsym value: 0.466 / % possible all: 94.3

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Processing

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

1w8a

5sxm

3g5c


Resolution: 3.49→42.46 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.95
RfactorNum. reflection% reflection
Rfree0.277 2892 4.96 %
Rwork0.236 --
obs0.238 58272 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.49→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23766 0 264 196 24226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324624
X-RAY DIFFRACTIONf_angle_d0.83233369
X-RAY DIFFRACTIONf_dihedral_angle_d12.1914844
X-RAY DIFFRACTIONf_chiral_restr0.063696
X-RAY DIFFRACTIONf_plane_restr0.0064266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.540.37481170.32212310X-RAY DIFFRACTION88
3.5428-3.60390.36821260.30282611X-RAY DIFFRACTION98
3.6039-3.66940.37611550.28692659X-RAY DIFFRACTION98
3.6694-3.73990.30651480.29792575X-RAY DIFFRACTION97
3.7399-3.81620.33721280.28592615X-RAY DIFFRACTION98
3.8162-3.89910.331570.27192663X-RAY DIFFRACTION98
3.8991-3.98980.29811190.26952656X-RAY DIFFRACTION98
3.9898-4.08950.35131370.25812618X-RAY DIFFRACTION99
4.0895-4.19990.27911250.23732675X-RAY DIFFRACTION99
4.1999-4.32340.27631210.23722682X-RAY DIFFRACTION98
4.3234-4.46280.27781230.22512654X-RAY DIFFRACTION99
4.4628-4.62210.25371310.22612695X-RAY DIFFRACTION97
4.6221-4.8070.28361280.20852610X-RAY DIFFRACTION99
4.807-5.02540.22841700.20832682X-RAY DIFFRACTION98
5.0254-5.28990.24481240.20512609X-RAY DIFFRACTION97
5.2899-5.62060.25921680.22542648X-RAY DIFFRACTION97
5.6206-6.05350.261490.23462672X-RAY DIFFRACTION98
6.0535-6.66060.26941410.24322638X-RAY DIFFRACTION96
6.6606-7.61950.27661300.24432655X-RAY DIFFRACTION95
7.6195-9.58160.24091510.22482662X-RAY DIFFRACTION94
9.5816-42.460.24731440.1932791X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -18.7544 Å / Origin y: -6.8129 Å / Origin z: -24.0239 Å
111213212223313233
T0.5613 Å2-0.012 Å20.0252 Å2-0.4941 Å2-0.0534 Å2--0.5393 Å2
L0.0824 °20.006 °20.0531 °2-0.1501 °2-0.0521 °2--0.1685 °2
S-0.0176 Å °0.0268 Å °0.0723 Å °-0.1055 Å °0.0282 Å °0.0065 Å °-0.1531 Å °0.0687 Å °-0.0082 Å °
Refinement TLS groupSelection details: ALL

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