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- PDB-2pnt: Crystal structure of the PDZ domain of human GRASP (GRP1) in comp... -

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Basic information

Entry
Database: PDB / ID: 2pnt
TitleCrystal structure of the PDZ domain of human GRASP (GRP1) in complex with the C-terminal peptide of the metabotropic glutamate receptor type 1
ComponentsGeneral receptor for phosphoinositides 1-associated scaffold protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Scaffold protein / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / protein localization / postsynaptic membrane / postsynaptic density / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction ...small GTPase binding => GO:0031267 / regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / protein localization / postsynaptic membrane / postsynaptic density / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsElkins, J. / Papagrigoriou, E. / Cooper, C. / Gileadi, C. / Uppenberg, J. / Bray, J. / von Delft, F. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. ...Elkins, J. / Papagrigoriou, E. / Cooper, C. / Gileadi, C. / Uppenberg, J. / Bray, J. / von Delft, F. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2010
Title: Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms
Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R. / Doyle, D.A.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 23, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE C-TERMINAL RESIDUES 189-192 (SER-SER-THR-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN ...SEQUENCE C-TERMINAL RESIDUES 189-192 (SER-SER-THR-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN METABOTROPIC GLUTAMATE RECEPTOR 1, UNIPROT ENTRY MGR1_HUMAN, ACCESSION CODE Q13255, SEQUENCE POSITION 1191-1194.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General receptor for phosphoinositides 1-associated scaffold protein
B: General receptor for phosphoinositides 1-associated scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1403
Polymers22,1052
Non-polymers351
Water1,36976
1
A: General receptor for phosphoinositides 1-associated scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0882
Polymers11,0521
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General receptor for phosphoinositides 1-associated scaffold protein


Theoretical massNumber of molelcules
Total (without water)11,0521
Polymers11,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.288, 72.288, 163.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsTwo biological units can be found in the ASU

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Components

#1: Protein General receptor for phosphoinositides 1-associated scaffold protein / GRP1-associated scaffold protein


Mass: 11052.468 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRASP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) with pRARE plasmid / References: UniProt: Q7Z6J2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 1.26M NaH2PO4, 0.14M K2HPO4, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.035 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.148→62.622 Å / Num. all: 14546 / Num. obs: 14546 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.148→2.23 Å / Redundancy: 6.5 % / Num. unique all: 1411 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1GQ4, 2OCS

1gq4

2ocs


Resolution: 2.148→62.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.029 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23198 729 5 %RANDOM
Rwork0.20876 ---
all0.20995 13758 --
obs0.20995 13758 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.148→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 1 76 1491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211434
X-RAY DIFFRACTIONr_bond_other_d0.0010.02925
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9591946
X-RAY DIFFRACTIONr_angle_other_deg0.92332273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89924.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34215243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.675158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined0.1970.2246
X-RAY DIFFRACTIONr_nbd_other0.1980.2936
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2668
X-RAY DIFFRACTIONr_nbtor_other0.0890.2851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9191.5942
X-RAY DIFFRACTIONr_mcbond_other0.2011.5379
X-RAY DIFFRACTIONr_mcangle_it1.61221482
X-RAY DIFFRACTIONr_scbond_it2.543539
X-RAY DIFFRACTIONr_scangle_it3.9344.5463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.148→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 57 -
Rwork0.282 979 -
obs--99.04 %

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