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- PDB-3jxt: Crystal structure of the third PDZ domain of SAP-102 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3jxt
TitleCrystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand
Components
  • Disks large homolog 3
  • Voltage-dependent calcium channel gamma-2 subunit
KeywordsSIGNALING PROTEIN / SAP102 / DLG3 / Stargazin / 4-DMAP / 4DB / PDZ domain / solvatochromic flurophore / fluorogenic probe / Calcium channel / Calcium transport / Ion transport / Ionic channel / Transport / Voltage-gated channel
Function / homology
Function and homology information


negative regulation of phosphatase activity / Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / Trafficking of AMPA receptors / establishment of planar polarity / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / Neurexins and neuroligins / : ...negative regulation of phosphatase activity / Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / Trafficking of AMPA receptors / establishment of planar polarity / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / Neurexins and neuroligins / : / structural constituent of postsynaptic density / receptor localization to synapse / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / regulation of AMPA receptor activity / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor internalization / channel regulator activity / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / Synaptic adhesion-like molecules / nervous system process / RAF/MAP kinase cascade / protein targeting to membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / voltage-gated calcium channel complex / neuromuscular junction development / transmission of nerve impulse / regulation of postsynaptic membrane neurotransmitter receptor levels / receptor clustering / membrane depolarization / AMPA glutamate receptor complex / positive regulation of protein tyrosine kinase activity / voltage-gated calcium channel activity / bicellular tight junction / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / phosphatase binding / somatodendritic compartment / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / PDZ domain binding / regulation of membrane potential / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / kinase binding / cell-cell adhesion / response to calcium ion / cell-cell junction / cell junction / growth cone / basolateral plasma membrane / protein phosphatase binding / postsynaptic density / protein domain specific binding / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Disks Large homologue 3, SH3 domain / Voltage-dependent calcium channel, gamma-2 subunit / 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 / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit ...Disks Large homologue 3, SH3 domain / Voltage-dependent calcium channel, gamma-2 subunit / 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 / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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. / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Voltage-dependent calcium channel gamma-2 subunit / Disks large homolog 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSainlos, M. / Olivier, N.B. / Imperiali, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Caged mono- and divalent ligands for light-assisted disruption of PDZ domain-mediated interactions.
Authors: Sainlos, M. / Iskenderian-Epps, W.S. / Olivier, N.B. / Choquet, D. / Imperiali, B.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 3
B: Disks large homolog 3
C: Voltage-dependent calcium channel gamma-2 subunit
D: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0965
Polymers24,0374
Non-polymers591
Water6,125340
1
A: Disks large homolog 3
D: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0773
Polymers12,0182
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-2.9 kcal/mol
Surface area5780 Å2
MethodPISA
2
B: Disks large homolog 3
C: Voltage-dependent calcium channel gamma-2 subunit


Theoretical massNumber of molelcules
Total (without water)12,0182
Polymers12,0182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2.5 kcal/mol
Surface area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.597, 54.215, 86.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the monomeric complex composed of one PDZ domain and its ligand.

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Components

#1: Protein Disks large homolog 3 / Synapse-associated protein 102 / SAP102 / PSD-95/SAP90-related protein 1


Mass: 11145.364 Da / Num. of mol.: 2 / Fragment: Third PDZ domain: UNP residues 393-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg3, Dlgh3 / Plasmid: pET-NO, modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q62936
#2: Protein/peptide Voltage-dependent calcium channel gamma-2 subunit / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin


Mass: 872.987 Da / Num. of mol.: 2
Fragment: C-terminal motif of Stargazin: UNP O88602 residues 318-323
Mutation: R318(4DB) / Source method: obtained synthetically
Details: Peptide ligand obtained by solid phase peptide synthesis
References: UniProt: O88602
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 7, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 37896 / Num. obs: 37820 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 16.346 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.19
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.94 / Num. unique all: 3720 / Rsym value: 0.24 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JVQ

3jvq
PDB Unreleased entry


Resolution: 1.5→45.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21442 1886 5 %RANDOM
Rwork0.18511 ---
all0.18659 35937 --
obs0.18659 35869 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 4 340 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0221572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.28922117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4155196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.84122.20668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01215245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5691518
X-RAY DIFFRACTIONr_chiral_restr0.060.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021207
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3160.2757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21055
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1931.5996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.40821572
X-RAY DIFFRACTIONr_scbond_it4.6443576
X-RAY DIFFRACTIONr_scangle_it6.7954.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 125 -
Rwork0.246 2604 -
obs--100 %

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