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- PDB-2jil: Crystal structure of 2nd PDZ domain of glutamate receptor interac... -

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Basic information

Entry
Database: PDB / ID: 2jil
TitleCrystal structure of 2nd PDZ domain of glutamate receptor interacting protein-1 (GRIP1)
ComponentsGLUTAMATE RECEPTOR INTERACTING PROTEIN-1
KeywordsMEMBRANE PROTEIN / ENDOPLASMIC RETICULUM / POSTSYNAPTIC MEMBRANE / MEMBRANE
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / beta-catenin binding / signaling receptor complex adaptor activity / cytoplasmic vesicle / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density ...Trafficking of GluR2-containing AMPA receptors / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / beta-catenin binding / signaling receptor complex adaptor activity / cytoplasmic vesicle / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / intracellular signal transduction / dendrite / endoplasmic reticulum membrane / plasma membrane / cytosol
Similarity search - Function
Glutamate receptor-interacting protein 1/2 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Glutamate receptor-interacting protein 1/2 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Glutamate receptor-interacting protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Tickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.
CitationJournal: To be Published
Title: Crystal Structure of 2Nd Pdz Domain of Glutamate Receptor Interacting Protein-1 (Grip1)
Authors: Tickle, J. / Elkins, J. / Pike, A.C.W. / Cooper, C. / Salah, E. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR INTERACTING PROTEIN-1
B: GLUTAMATE RECEPTOR INTERACTING PROTEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1627
Polymers20,8602
Non-polymers3025
Water2,720151
1
A: GLUTAMATE RECEPTOR INTERACTING PROTEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6084
Polymers10,4301
Non-polymers1783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUTAMATE RECEPTOR INTERACTING PROTEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5543
Polymers10,4301
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.060, 61.057, 96.397
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-2010-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.08357, 0.99649, -0.00491), (0.99587, 0.08369, 0.03518), (0.03546, -0.00195, -0.99937)
Vector: 28.96959, 1.05976, 23.91029)

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Components

#1: Protein GLUTAMATE RECEPTOR INTERACTING PROTEIN-1 / GRIP1 PROTEIN


Mass: 10429.821 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN 2, RESIDUES 149-239 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9Y3R0
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 184 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 184 TO SER

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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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5
Details: 20% PEG3350, 0.20M POTASSIUM THIOCYANATE, 10% ETHYLENE GLYCOL, 0.1M BIS TRIS PROPANE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.5→41.31 Å / Num. obs: 26857 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 21.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F

1n7e

1tq3

1be9

1mfg

2he2

1n7f


Resolution: 1.5→48.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.642 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2226 8.3 %RANDOM
Rwork0.189 ---
obs0.192 24603 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--0.19 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 18 151 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211487
X-RAY DIFFRACTIONr_bond_other_d0.0040.021020
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9812004
X-RAY DIFFRACTIONr_angle_other_deg1.67832490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30621.72458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6491518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_nbd_refined0.2640.2306
X-RAY DIFFRACTIONr_nbd_other0.2280.21077
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2706
X-RAY DIFFRACTIONr_nbtor_other0.0870.2854
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3770.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6463960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.03551552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1468527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.43711450
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.403 166
Rwork0.314 1792
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)
10.8740.01660.38683.99280.75462.61010.020.2144-0.0857-0.181-0.25180.2378-0.1133-0.34230.2318-0.1571-0.013-0.0049-0.0509-0.0494-0.095810.82156.970911.5215
24.39020.3029-0.5280.9962-0.22981.9275-0.11710.0613-0.1948-0.07280.1167-0.13630.28590.17760.0004-0.0514-0.00510.0106-0.1381-0.0149-0.14935.241613.101513.0577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 243
2X-RAY DIFFRACTION2B-1 - 243

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