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- PDB-5y31: Crystal structure of human LGI1-ADAM22 complex -

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Basic information

Entry
Database: PDB / ID: 5y31
TitleCrystal structure of human LGI1-ADAM22 complex
Components
  • Disintegrin and metalloproteinase domain-containing protein 22
  • Leucine-rich glioma-inactivated protein 1
KeywordsCELL ADHESION / epilepsy / synapse / ADAM / EPTP / WD40
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 / central nervous system development / axon guidance / 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 / central nervous system development / axon guidance / postsynaptic density membrane / 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. ...: / 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: 7.125 Å
AuthorsYamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22.
Authors: Yamagata, A. / Miyazaki, Y. / Yokoi, N. / Shigematsu, H. / Sato, Y. / Goto-Ito, S. / Maeda, A. / Goto, T. / Sanbo, M. / Hirabayashi, M. / Shirouzu, M. / Fukata, Y. / Fukata, M. / Fukai, S.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)237,28122
Polymers234,7484
Non-polymers2,53318
Water00
1
A: Disintegrin and metalloproteinase domain-containing protein 22
B: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,64011
Polymers117,3742
Non-polymers1,2669
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Disintegrin and metalloproteinase domain-containing protein 22
D: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,64011
Polymers117,3742
Non-polymers1,2669
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.143, 124.324, 164.663
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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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: 54803.230 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 233-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM22, MDC2 / Production host: Mammalia (mammals) / References: UniProt: Q9P0K1
#2: Protein Leucine-rich glioma-inactivated protein 1 / Epitempin-1


Mass: 62570.785 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 37-557 / Mutation: R470A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGI1, EPT, UNQ775/PRO1569 / Production host: Mammalia (mammals) / References: UniProt: O95970
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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

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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: 4.39 Å3/Da / Density % sol: 71.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.12→50 Å / Num. obs: 6092 / % possible obs: 97.9 % / Redundancy: 7.1 % / Net I/σ(I): 13.3
Reflection shellResolution: 7.12→7.24 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.6 / CC1/2: 0.578 / Rsym value: 0.461 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.125→48.993 Å / SU ML: 1.37 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 37.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3163 297 4.88 %
Rwork0.2653 --
obs0.2676 6086 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.125→48.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15684 0 148 0 15832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416279
X-RAY DIFFRACTIONf_angle_d0.81921878
X-RAY DIFFRACTIONf_dihedral_angle_d12.5315914
X-RAY DIFFRACTIONf_chiral_restr0.0372424
X-RAY DIFFRACTIONf_plane_restr0.0032810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.1255-8.96840.40461420.3162829X-RAY DIFFRACTION96
8.9684-48.99380.28781550.24692960X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.1416 Å / Origin y: -1.187 Å / Origin z: 51.1431 Å
111213212223313233
T4.4121 Å20.0583 Å2-0.0416 Å2-3.7659 Å2-0.1017 Å2--4.3694 Å2
L0.7573 °20.0663 °2-0.4651 °2-0.3956 °2-0.0649 °2---0.0244 °2
S0.092 Å °0.4117 Å °0.1372 Å °0.0921 Å °-0.2018 Å °-0.0261 Å °0.4914 Å °0.155 Å °0.0103 Å °
Refinement TLS groupSelection details: all

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