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- PDB-4oaj: Crystal structure of the complex between SAP97 PDZ2 and 5HT2A rec... -

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Basic information

Entry
Database: PDB / ID: 4oaj
TitleCrystal structure of the complex between SAP97 PDZ2 and 5HT2A receptor peptide
Components
  • 5-hydroxytryptamine receptor 2A peptide
  • Disks large homolog 1
KeywordsPROTEIN BINDING / PDZ domain / 5HT2A receptor
Function / homology
Function and homology information


Serotonin receptors / tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / Activation of Ca-permeable Kainate Receptor / regulation of potassium ion export across plasma membrane / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation ...Serotonin receptors / tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / Activation of Ca-permeable Kainate Receptor / regulation of potassium ion export across plasma membrane / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / membrane raft organization / sensory perception of temperature stimulus / protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Trafficking of AMPA receptors / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / establishment of centrosome localization / neurofilament / myelin sheath abaxonal region / structural constituent of postsynaptic density / RAF/MAP kinase cascade / embryonic skeletal system morphogenesis / epithelial structure maintenance / reproductive structure development / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / immunological synapse formation / peristalsis / astral microtubule organization / cell body fiber / lateral loop / phospholipase C-activating serotonin receptor signaling pathway / artery smooth muscle contraction / smooth muscle tissue development / positive regulation of cytokine production involved in immune response / cell projection membrane / serotonin receptor activity / bicellular tight junction assembly / G protein-coupled serotonin receptor activity / cortical microtubule organization / paranode region of axon / sensitization / serotonin receptor signaling pathway / positive regulation of developmental growth / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / urinary bladder smooth muscle contraction / neurotransmitter receptor activity / hard palate development / serotonin binding / positive regulation of multicellular organism growth / node of Ranvier / positive regulation of platelet aggregation / amyloid precursor protein metabolic process / endothelial cell proliferation / negative regulation of synaptic transmission, glutamatergic / lens development in camera-type eye / G alpha (q) signalling events / cortical actin cytoskeleton organization / ureteric bud development / regulation of myelination / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / branching involved in ureteric bud morphogenesis / temperature homeostasis / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of vasoconstriction / microvillus / detection of temperature stimulus involved in sensory perception of pain / positive regulation of actin filament polymerization / regulation of dopamine secretion / negative regulation of potassium ion transport / protein tyrosine kinase activator activity / basement membrane / immunological synapse / lateral plasma membrane / positive regulation of execution phase of apoptosis / bicellular tight junction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / potassium channel regulator activity / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of fat cell differentiation / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / behavioral response to cocaine / actin filament polymerization / release of sequestered calcium ion into cytosol / presynaptic modulation of chemical synaptic transmission / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization / synaptic membrane / T cell activation / positive regulation of glycolytic process / dendritic shaft
Similarity search - Function
L27-1 / L27_1 / 5-Hydroxytryptamine 2A receptor / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK ...L27-1 / L27_1 / 5-Hydroxytryptamine 2A receptor / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 / 5-hydroxytryptamine receptor family / : / 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. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
5-hydroxytryptamine receptor 2A / Disks large homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPandalaneni, S. / Dorr, L. / Mayans, O. / Lian, L.-Y.
CitationJournal: To be Published
Title: Crystal structure of the complex between SAP97 PDZ2 and 5HT2A receptor peptide
Authors: Pandalaneni, S. / Dorr, L. / Mayans, O. / Lian, L.-Y.
History
DepositionJan 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 1
B: 5-hydroxytryptamine receptor 2A peptide


Theoretical massNumber of molelcules
Total (without water)10,4352
Polymers10,4352
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.000, 45.000, 88.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Disks large homolog 1 / Embryo-dlg/synapse-associated protein 97 / E-dlg/SAP97 / Synapse-associated protein 97 / SAP-97 / SAP97


Mass: 9656.164 Da / Num. of mol.: 1 / Fragment: PDZ 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dlg1, Dlgh1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q811D0
#2: Protein/peptide 5-hydroxytryptamine receptor 2A peptide


Mass: 778.894 Da / Num. of mol.: 1 / Fragment: UNP residues 465-471 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P14842
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 3.2M Ammonium Sulfate, 0.1M Citric Acid pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→29.189 Å / Num. obs: 4904 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.85 % / Biso Wilson estimate: 46.23 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.71
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 8.64 % / Mean I/σ(I) obs: 3.76 / Num. unique all: 299 / Rsym value: 0.655 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.189 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 253 5.16 %random
Rwork0.2054 ---
obs0.2079 4904 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 0 14 744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008738
X-RAY DIFFRACTIONf_angle_d1.103994
X-RAY DIFFRACTIONf_dihedral_angle_d16.477271
X-RAY DIFFRACTIONf_chiral_restr0.071120
X-RAY DIFFRACTIONf_plane_restr0.004126
LS refinement shellResolution: 2.3→2.8974 Å
RfactorNum. reflection% reflection
Rfree0.3299 135 -
Rwork0.2356 2255 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -4.3859 Å / Origin y: 14.3691 Å / Origin z: 13.2993 Å
111213212223313233
T0.3355 Å2-0.0366 Å2-0.0221 Å2-0.8133 Å2-0.0856 Å2--0.4718 Å2
L1.3895 °2-1.8835 °2-1.166 °2-4.8822 °2-1.744 °2--8.334 °2
S0.2556 Å °0.4573 Å °0.0716 Å °-0.2641 Å °-0.3492 Å °-0.0484 Å °0.3872 Å °0.0979 Å °0.0768 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 315:406 ) OR ( CHAIN B AND RESID 14:20 )A315 - 406
2X-RAY DIFFRACTION1( CHAIN A AND RESID 315:406 ) OR ( CHAIN B AND RESID 14:20 )B14 - 20

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