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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


dendritic microtubule / retrograde axonal protein transport / negative regulation of protein localization to microtubule / RHO GTPases activate CIT / voluntary musculoskeletal movement / neuronal ion channel clustering / positive regulation of AMPA glutamate receptor clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding ...dendritic microtubule / retrograde axonal protein transport / negative regulation of protein localization to microtubule / RHO GTPases activate CIT / voluntary musculoskeletal movement / neuronal ion channel clustering / positive regulation of AMPA glutamate receptor clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / anterograde axonal protein transport / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / photoreceptor cell maintenance / cytoskeletal adaptor activity / positive regulation of protein localization to cell surface / protein localization to synapse / cerebellar mossy fiber / dendritic spine morphogenesis / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / proximal dendrite / negative regulation of receptor internalization / vocalization behavior / axon initial segment / juxtaparanode region of axon / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of synapse assembly / neuromuscular process controlling balance / positive regulation of dendrite morphogenesis / acetylcholine receptor binding / frizzled binding / cellular response to potassium ion / dendritic spine organization / regulation of NMDA receptor activity / RAF/MAP kinase cascade / NMDA selective glutamate receptor signaling pathway / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / neuron projection terminus / cortical cytoskeleton / AMPA glutamate receptor clustering / locomotory exploration behavior / social behavior / regulation of neuronal synaptic plasticity / associative learning / AMPA glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / photoreceptor outer segment / kinesin binding / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of protein localization / axon cytoplasm / neuron projection maintenance / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / sensory perception of sound / ionotropic glutamate receptor binding / dendrite cytoplasm / excitatory synapse / positive regulation of excitatory postsynaptic potential / cell periphery / neuron cellular homeostasis / synaptic membrane / PDZ domain binding / neuromuscular junction / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / cerebral cortex development / tubulin binding / memory / regulation of synaptic plasticity / microtubule cytoskeleton organization / cell junction / postsynaptic density membrane / kinase binding / cell-cell junction / nervous system development / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / actin binding / protein-containing complex assembly / scaffold protein binding / chemical synaptic transmission / protein phosphatase binding / microtubule binding / dendritic spine / postsynaptic membrane / postsynapse / postsynaptic density
Similarity search - Function
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 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

Downloads & links

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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


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