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- PDB-2qt5: Crystal Structure of GRIP1 PDZ12 in Complex with the Fras1 Peptide -

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Basic information

Entry
Database: PDB / ID: 2qt5
TitleCrystal Structure of GRIP1 PDZ12 in Complex with the Fras1 Peptide
Components
  • (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
  • Glutamate receptor-interacting protein 1
KeywordsPEPTIDE BINDING PROTEIN / PDZ-Peptide Complex / PDZ Tandem / Alternative splicing / Cell junction / Cytoplasm / Endoplasmic reticulum / Membrane / Postsynaptic cell membrane / Synapse / PROTEIN BINDING
Function / homology
Function and homology information


regulation of synaptic scaling / exocyst / vesicle-mediated transport in synapse / dendrite arborization / proximal dendrite / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / spine synapse ...regulation of synaptic scaling / exocyst / vesicle-mediated transport in synapse / dendrite arborization / proximal dendrite / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / spine synapse / dendritic spine neck / dendritic spine head / presynaptic active zone / Trafficking of GluR2-containing AMPA receptors / GABA-ergic synapse / synaptic cleft / cellular response to brain-derived neurotrophic factor stimulus / dendritic shaft / synaptic membrane / PDZ domain binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / protein localization / terminal bouton / recycling endosome / cerebral cortex development / presynapse / GTPase binding / presynaptic membrane / nervous system development / postsynapse / postsynaptic membrane / perikaryon / microtubule / dendritic spine / postsynaptic density / neuron projection / membrane raft / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / plasma membrane
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
ACETIC ACID / Glutamate receptor-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLong, J. / Wei, Z. / Feng, W. / Zhao, Y. / Zhang, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Supramodular nature of GRIP1 revealed by the structure of its PDZ12 tandem in complex with the carboxyl tail of Fras1.
Authors: Long, J. / Wei, Z. / Feng, W. / Yu, C. / Zhao, Y.X. / Zhang, M.
History
DepositionAug 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Glutamate receptor-interacting protein 1
B: Glutamate receptor-interacting protein 1
X: (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
Y: (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1938
Polymers44,9494
Non-polymers2444
Water3,819212
1
A: Glutamate receptor-interacting protein 1
X: (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6575
Polymers22,4752
Non-polymers1823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint1 kcal/mol
Surface area10740 Å2
MethodPISA
2
B: Glutamate receptor-interacting protein 1
Y: (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,4752
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint1 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 75.925, 126.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor-interacting protein 1 / GRIP1 protein / AMPA receptor-interacting protein GRIP1


Mass: 21485.533 Da / Num. of mol.: 2 / Fragment: PDZ12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grip1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97879
#2: Protein/peptide (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL) / Fras1


Mass: 988.995 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: commercially synthesized
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate, 0.1M sodium cacodylate pH 6.5, 20% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.157 Å / Num. obs: 25986 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.425.60.3552.22067437000.35599.8
2.42-2.578.50.2852.73004835370.285100
2.57-2.758.70.1963.92913333460.196100
2.75-2.978.70.1216.32697430930.121100
2.97-3.258.70.07610.12521228860.076100
3.25-3.648.70.04516.62269126050.045100
3.64-4.28.60.03123.12028323460.031100
4.2-5.148.60.02232.51695019750.022100
5.14-7.278.40.02330.21327815740.023100
7.27-37.967.10.0249.965679240.02498.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.423 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1344 5.2 %RANDOM
Rwork0.199 ---
obs0.202 25976 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 8 220 3236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223059
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9874124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23423.81126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00215560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022257
X-RAY DIFFRACTIONr_nbd_refined0.1790.21186
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.223
X-RAY DIFFRACTIONr_mcbond_it1.14822011
X-RAY DIFFRACTIONr_mcangle_it1.99233162
X-RAY DIFFRACTIONr_scbond_it2.60741129
X-RAY DIFFRACTIONr_scangle_it4.126957
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 102 -
Rwork0.235 1747 -
all-1849 -
obs--99.46 %

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