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- PDB-5gnv: Structure of PSD-95/MAP1A complex reveals unique target recogniti... -

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Basic information

Entry
Database: PDB / ID: 5gnv
TitleStructure of PSD-95/MAP1A complex reveals unique target recognition mode of MAGUK GK domain
Components
  • Disks large homolog 4
  • Microtubule-associated protein 1A
KeywordsPEPTIDE BINDING PROTEIN / binding-induced folding
Function / homology
Function and homology information


primary dendrite / dendritic microtubule / regulation of microtubule depolymerization / retrograde axonal protein transport / negative regulation of protein localization to microtubule / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins ...primary dendrite / dendritic microtubule / regulation of microtubule depolymerization / retrograde axonal protein transport / negative regulation of protein localization to microtubule / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / anterograde axonal protein transport / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / axon initial segment / voluntary musculoskeletal movement / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / cytoskeletal anchor activity / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / negative regulation of microtubule depolymerization / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / positive regulation of protein localization to cell surface / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / frizzled binding / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / photoreceptor cell maintenance / neuron projection terminus / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / microtubule associated complex / beta-2 adrenergic receptor binding / positive regulation of protein localization / cortical cytoskeleton / dendrite development / regulation of neuronal synaptic plasticity / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / kinesin binding / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / photoreceptor outer segment / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / axon cytoplasm / ionotropic glutamate receptor binding / collagen binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / neuron projection maintenance / axonogenesis / tubulin binding / dendritic shaft / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / sensory perception of sound / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / memory / microtubule cytoskeleton organization / cerebral cortex development / kinase binding / neuron cellular homeostasis / cell-cell junction / synaptic vesicle / cell junction / actin binding / positive regulation of cytosolic calcium ion concentration
Similarity search - Function
Microtubule associated protein 1A / Microtubule associated protein 1 / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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 / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...Microtubule associated protein 1A / Microtubule associated protein 1 / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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 / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / PDZ domain / SH3 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disks large homolog 4 / Microtubule-associated protein 1A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsShang, Y. / Xia, Y. / Zhu, R. / Zhu, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470733 China
the Shanghai YangFan Plan for Young Scientists14YF1406700 China
the SIBS Frontier Science Program for talented young scientists2014KIP101 China
CitationJournal: Biochem. J. / Year: 2017
Title: Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain
Authors: Xia, Y. / Shang, Y. / Zhang, R. / Zhu, J.
History
DepositionJul 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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
B: Microtubule-associated protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6824
Polymers24,4892
Non-polymers1922
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-17 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.445, 156.861, 59.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-801-

SO4

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Components

#1: Protein Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90


Mass: 21690.418 Da / Num. of mol.: 1 / Fragment: UNP residues 531-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31016
#2: Protein/peptide Microtubule-associated protein 1A / MAP-1A


Mass: 2798.969 Da / Num. of mol.: 1 / Fragment: UNP residues 1866-1891 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QYR6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.5
Details: 0.2M lithium sulfate, 0.1M Bis-Tris pH 6.5 and 25%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9354 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 31.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.596→40.089 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 443 4.75 %
Rwork0.2152 --
obs0.2171 9335 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.596→40.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 10 36 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111605
X-RAY DIFFRACTIONf_angle_d1.4912169
X-RAY DIFFRACTIONf_dihedral_angle_d22.008594
X-RAY DIFFRACTIONf_chiral_restr0.102234
X-RAY DIFFRACTIONf_plane_restr0.007288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5962-2.97170.32961520.27442884X-RAY DIFFRACTION99
2.9717-3.74360.32151460.22382935X-RAY DIFFRACTION100
3.7436-40.09390.21081450.19883073X-RAY DIFFRACTION100

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