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- PDB-2i1n: Crystal structure of the 1st PDZ domain of Human DLG3 -

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Basic information

Entry
Database: PDB / ID: 2i1n
TitleCrystal structure of the 1st PDZ domain of Human DLG3
ComponentsDiscs, large homolog 3
KeywordsSIGNALING PROTEIN / DLG3 / PDZ / PDZ domain / signal transduction / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


establishment of planar polarity / NrCAM interactions / receptor localization to synapse / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering ...establishment of planar polarity / NrCAM interactions / receptor localization to synapse / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / bicellular tight junction / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatase binding / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / adherens junction / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / nervous system development / RAF/MAP kinase cascade / basolateral plasma membrane / chemical synaptic transmission / neuron projection / negative regulation of cell population proliferation / ubiquitin protein ligase binding / protein kinase binding / glutamatergic synapse / extracellular space / plasma membrane / cytosol
Similarity search - Function
Disks Large homologue 3, SH3 domain / 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. ...Disks Large homologue 3, SH3 domain / 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
Disks large homolog 3 / Disks large homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTurnbull, A.P. / Phillips, C. / Bunkoczi, G. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Gorrec, F. / Umeano, C. / Elkins, J. / Berridge, G. ...Turnbull, A.P. / Phillips, C. / Bunkoczi, G. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Gorrec, F. / Umeano, C. / Elkins, J. / Berridge, G. / Savitsky, P. / Gileadi, O. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Discs, large homolog 3
B: Discs, large homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9787
Polymers21,8632
Non-polymers1155
Water3,387188
1
A: Discs, large homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9542
Polymers10,9311
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Discs, large homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0235
Polymers10,9311
Non-polymers924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Discs, large homolog 3
B: Discs, large homolog 3
hetero molecules

A: Discs, large homolog 3
B: Discs, large homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,95614
Polymers43,7264
Non-polymers23010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6080 Å2
ΔGint-117 kcal/mol
Surface area20370 Å2
MethodPISA
4
A: Discs, large homolog 3
B: Discs, large homolog 3
hetero molecules

A: Discs, large homolog 3
B: Discs, large homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,95614
Polymers43,7264
Non-polymers23010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6600 Å2
ΔGint-92 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.817, 80.545, 67.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Discs, large homolog 3 / Neuroendocrine-dlg / Drosophila / Synapse- associated protein 102


Mass: 10931.439 Da / Num. of mol.: 2 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: Q5JUW7, UniProt: Q92796*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0M LiSO4; 0.5M TMAO, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 19545 / Num. obs: 19545 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID = 2FE5

2fe5


Resolution: 1.85→29.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.292 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21775 989 5.1 %RANDOM
Rwork0.18585 ---
all0.18746 18371 --
obs0.18746 18371 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.313 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2---0.99 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 5 188 1694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221549
X-RAY DIFFRACTIONr_bond_other_d0.0040.021049
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9862115
X-RAY DIFFRACTIONr_angle_other_deg0.99932567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1525209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.43864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0021515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_nbd_refined0.2060.2243
X-RAY DIFFRACTIONr_nbd_other0.210.21103
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2754
X-RAY DIFFRACTIONr_nbtor_other0.0830.2830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.681.51021
X-RAY DIFFRACTIONr_mcbond_other0.1611.5414
X-RAY DIFFRACTIONr_mcangle_it1.19921662
X-RAY DIFFRACTIONr_scbond_it1.8333530
X-RAY DIFFRACTIONr_scangle_it3.144.5449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 71 -
Rwork0.241 1266 -
obs--95.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7726-0.76470.32982.35610.23861.47970.06830.1106-0.0041-0.18090.0032-0.06960.12770.1253-0.0715-0.031-0.0038-0.0158-0.10520.0155-0.120119.95910.467813.3436
21.98640.5731-0.85142.75290.71651.74760.03090.03260.0694-0.023-0.0420.00250.03370.13340.011-0.11710.02750.0154-0.13920.0132-0.158929.2216.08230.3991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA126 - 2262 - 102
2X-RAY DIFFRACTION2BB126 - 2262 - 102

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