[English] 日本語
Yorodumi
- PDB-1n7e: Crystal structure of the sixth PDZ domain of GRIP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n7e
TitleCrystal structure of the sixth PDZ domain of GRIP1
ComponentsAMPA receptor interacting protein GRIP
KeywordsPROTEIN BINDING / PDZ / grip
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
Glutamate receptor-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsIm, Y.J. / Park, S.H. / Rho, S.H. / Lee, J.H. / Kang, G.B. / Sheng, M. / Kim, E. / Eom, S.H.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization
Authors: Im, Y.J. / Park, S.H. / Rho, S.H. / Lee, J.H. / Kang, G.B. / Sheng, M. / Kim, E. / Eom, S.H.
History
DepositionNov 14, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMPA receptor interacting protein GRIP


Theoretical massNumber of molelcules
Total (without water)10,1431
Polymers10,1431
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.267, 40.267, 222.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein AMPA receptor interacting protein GRIP / glutamate receptor interacting protein 1


Mass: 10142.639 Da / Num. of mol.: 1 / Fragment: sixth PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grip1 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97879
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Park, S.H., (2002) Acta Cryst., D58, 1063.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 154604 / Num. obs: 151976 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.36 / % possible all: 93.3
Reflection
*PLUS
Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 93.3 % / Rmerge(I) obs: 0.36

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→14.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 528947.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure was solved by Br-MAD phasing at the resolution of 1.9 angstrom, and it was refined using this data set.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1733 9.8 %RANDOM
Rwork0.254 ---
all0.256 154604 --
obs0.254 17694 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.1453 Å2 / ksol: 0.439491 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å21.25 Å20 Å2
2--3.6 Å20 Å2
3----7.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.5→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 0 141 841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 250 9.2 %
Rwork0.354 2478 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more