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- PDB-7cqf: Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 7cqf
TitleCrystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide
ComponentsDisks large homolog 4,Disintegrin and metalloproteinase domain-containing protein 22
KeywordsSIGNALING PROTEIN / Scaffold protein / Membrane receptor
Function / homology
Function and homology information


RHO GTPases activate CIT / LGI-ADAM interactions / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation ...RHO GTPases activate CIT / LGI-ADAM interactions / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / AMPA glutamate receptor clustering / Activation of Ca-permeable Kainate Receptor / cellular response to potassium ion / dendritic branch / positive regulation of dendrite morphogenesis / negative regulation of cell adhesion / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / D1 dopamine receptor binding / glutamate receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / central nervous system development / cell periphery / PDZ domain binding / establishment of protein localization / synaptic membrane / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / cerebral cortex development / metalloendopeptidase activity / kinase binding / integrin binding / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / cell adhesion / axon / signaling receptor binding / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / proteolysis / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Polyubiquitination (PEST) N-terminal domain of MAGUK / Reprolysin (M12B) family zinc metalloprotease ...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 / Polyubiquitination (PEST) N-terminal domain of MAGUK / Reprolysin (M12B) family zinc metalloprotease / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disks large 1-like / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / EGF-like domain, extracellular / EGF-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Metallopeptidase, catalytic domain superfamily / PDZ domain / EGF-like domain signature 1. / SH3 domain / EGF-like domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CHOLINE ION / Disks large homolog 4 / Disintegrin and metalloproteinase domain-containing protein 22
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYamagata, A. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03983 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: LGI1-ADAM22-MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention.
Authors: Fukata, Y. / Chen, X. / Chiken, S. / Hirano, Y. / Yamagata, A. / Inahashi, H. / Sanbo, M. / Sano, H. / Goto, T. / Hirabayashi, M. / Kornau, H.C. / Pruss, H. / Nambu, A. / Fukai, S. / Nicoll, R.A. / Fukata, M.
History
DepositionAug 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 4,Disintegrin and metalloproteinase domain-containing protein 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8347
Polymers16,4461
Non-polymers3886
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint9 kcal/mol
Surface area6620 Å2
Unit cell
Length a, b, c (Å)63.961, 63.961, 48.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Disks large homolog 4,Disintegrin and metalloproteinase domain-containing protein 22 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90 / ADAM 22 / ...Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90 / ADAM 22 / Metalloproteinase-disintegrin ADAM22-3 / Metalloproteinase-like / disintegrin-like / and cysteine-rich protein 2


Mass: 16446.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein of PSD-95 PDZ3, linker, and ADAM22 C-terminal peptide
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human)
Gene: Dlg4, Dlgh4, Psd95, ADAM22, MDC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016, UniProt: Q9P0K1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.75 Å3/Da / Density % sol: 29.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M choline chloride, 0.1 M Tris-HCl (pH 7.5), 14 % (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 10624 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.134 / Rsym value: 0.13 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 532 / CC1/2: 0.944 / Rpim(I) all: 0.262 / Rrim(I) all: 0.791 / Rsym value: 0.745

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TP3

1tp3


Resolution: 1.8→36.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.781 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20513 548 5.2 %RANDOM
Rwork0.16684 ---
obs0.16893 10052 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.8→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 24 46 947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013915
X-RAY DIFFRACTIONr_bond_other_d0.0010.017876
X-RAY DIFFRACTIONr_angle_refined_deg1.661.6521225
X-RAY DIFFRACTIONr_angle_other_deg1.4131.5992018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.69721.29654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04615155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.496159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5212.962455
X-RAY DIFFRACTIONr_mcbond_other2.5112.961454
X-RAY DIFFRACTIONr_mcangle_it3.5484.408567
X-RAY DIFFRACTIONr_mcangle_other3.5494.408568
X-RAY DIFFRACTIONr_scbond_it4.083.691460
X-RAY DIFFRACTIONr_scbond_other4.0763.695461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3615.302659
X-RAY DIFFRACTIONr_long_range_B_refined8.07135.265951
X-RAY DIFFRACTIONr_long_range_B_other8.07135.248951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 37 -
Rwork0.264 728 -
obs--100 %

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