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- PDB-3i4w: Crystal Structure of the third PDZ domain of PSD-95 -

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Basic information

Entry
Database: PDB / ID: 3i4w
TitleCrystal Structure of the third PDZ domain of PSD-95
ComponentsDisks large homolog 4
KeywordsCELL ADHESION / alpha and beta protein / Cell junction / Cell membrane / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / neuron spine / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / AMPA glutamate receptor clustering / cellular response to potassium ion / dendritic spine morphogenesis / Trafficking of AMPA receptors / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Signaling by ERBB4 / neuromuscular process controlling balance / Long-term potentiation / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / learning / PDZ domain binding / adherens junction / establishment of protein localization / synaptic membrane / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / endocytic vesicle membrane / cell junction / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. ...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. / 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 / Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsCamara-Artigas, A. / Gavira, J.A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Novel conformational aspects of the third PDZ domain of the neuronal post-synaptic density-95 protein revealed from two 1.4A X-ray structures
Authors: Camara-Artigas, A. / Murciano-Calles, J. / Gavira, J.A. / Cobos, E.S. / Martinez, J.C.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 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 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Disks large homolog 4
C: Disks large homolog 4
D: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,87210
Polymers44,5184
Non-polymers3546
Water4,216234
1
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2483
Polymers11,1291
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1892
Polymers11,1291
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2483
Polymers11,1291
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1892
Polymers11,1291
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.322, 42.152, 47.602
Angle α, β, γ (deg.)90.000, 90.000, 92.080
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLYGLYAA305 - 3306 - 31
21GLUGLUGLYGLYBB305 - 3306 - 31
31GLUGLUGLYGLYCC305 - 3306 - 31
41GLUGLUGLYGLYDD305 - 3306 - 31
12GLYGLYPHEPHEAA335 - 40036 - 101
22GLYGLYPHEPHEBB335 - 40036 - 101
32GLYGLYPHEPHECC335 - 40036 - 101
42GLYGLYPHEPHEDD335 - 40036 - 101

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Components

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


Mass: 11129.489 Da / Num. of mol.: 4 / Fragment: Third PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78352
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: capillary contradiffusion / pH: 4.6
Details: 0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.35→47.619 Å / Num. all: 73746 / Num. obs: 67847 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 13.018 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.074
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.84 / Num. unique all: 6858 / Rsym value: 0.411 / % possible all: 92.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å14.9 Å
Translation2 Å14.9 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE9

1be9


Resolution: 1.35→47.619 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.959 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3424 5 %RANDOM
Rwork0.187 ---
all0.189 73746 --
obs0.189 67844 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.97 Å2 / Biso mean: 18.043 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.09 Å2-0.01 Å2
2--0.12 Å20.02 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.35→47.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 24 234 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223040
X-RAY DIFFRACTIONr_angle_refined_deg2.1631.9764081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80123.889144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72315503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9151528
X-RAY DIFFRACTIONr_chiral_restr0.1340.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212332
X-RAY DIFFRACTIONr_mcbond_it2.70421932
X-RAY DIFFRACTIONr_mcangle_it3.90833058
X-RAY DIFFRACTIONr_scbond_it3.9721108
X-RAY DIFFRACTIONr_scangle_it5.72831023
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 685 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.360.5
BMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.450.5
DMEDIUM POSITIONAL0.330.5
AMEDIUM THERMAL1.382
BMEDIUM THERMAL1.382
CMEDIUM THERMAL1.372
DMEDIUM THERMAL1.372
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 236 -
Rwork0.287 4714 -
all-4950 -
obs--91.4 %

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