[English] 日本語
Yorodumi
- PDB-1n7f: Crystal structure of the sixth PDZ domain of GRIP1 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n7f
TitleCrystal structure of the sixth PDZ domain of GRIP1 in complex with liprin C-terminal peptide
Components
  • 8-mer peptide from interacting protein (liprin)
  • AMPA receptor interacting protein GRIP
KeywordsPROTEIN BINDING / PDZ / grip / liprin
Function / homology
Function and homology information


regulation of synaptic scaling / exocyst / spine apparatus / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / dendrite arborization / vesicle-mediated transport in synapse / Serotonin Neurotransmitter Release Cycle / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane ...regulation of synaptic scaling / exocyst / spine apparatus / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / dendrite arborization / vesicle-mediated transport in synapse / Serotonin Neurotransmitter Release Cycle / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / cortical microtubule organization / Glutamate Neurotransmitter Release Cycle / proximal dendrite / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / negative regulation of stress fiber assembly / spine synapse / dendritic spine neck / dendritic spine head / presynaptic active zone / Trafficking of GluR2-containing AMPA receptors / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of protein localization to plasma membrane / synaptic cleft / GABA-ergic synapse / cellular response to brain-derived neurotrophic factor stimulus / ionotropic glutamate receptor binding / cell-matrix adhesion / dendritic shaft / synaptic membrane / PDZ domain binding / positive regulation of protein localization to plasma membrane / synapse organization / Schaffer collateral - CA1 synapse / terminal bouton / recycling endosome / cerebral cortex development / protein localization / GTPase binding / presynapse / presynaptic membrane / nervous system development / cell cortex / perikaryon / postsynaptic membrane / microtubule / postsynapse / dendritic spine / postsynaptic density / neuron projection / membrane raft / axon / signaling receptor binding / focal adhesion / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / Glutamate receptor-interacting protein 1/2 / LAR-interacting protein, Liprin / PDZ domain 6 / PDZ domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain ...Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / Glutamate receptor-interacting protein 1/2 / LAR-interacting protein, Liprin / PDZ domain 6 / PDZ domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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 / Liprin-alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
B: AMPA receptor interacting protein GRIP
C: 8-mer peptide from interacting protein (liprin)
D: 8-mer peptide from interacting protein (liprin)


Theoretical massNumber of molelcules
Total (without water)22,0874
Polymers22,0874
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.790, 117.790, 101.974
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

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


Mass: 10142.639 Da / Num. of mol.: 2 / 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: Protein/peptide 8-mer peptide from interacting protein (liprin)


Mass: 901.020 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence of this chemically synthetized octa peptide occurs in the C-termiuns of human liprin alpha protein
References: GenBank: 21707845, UniProt: Q13136*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.96 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG400, MPD, pH 5.5, 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: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 192446 / Num. obs: 191677 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.58 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.89 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.566 / % possible all: 97.3
Reflection shell
*PLUS
% possible obs: 97.3 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.26 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure solved by Br-MAD phasing of peptide free crystal
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1822 7.3 %RANDOM
Rwork0.2 ---
all0.2024 ---
obs0.2 24896 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4386 Å2 / ksol: 0.35575 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å2-0.88 Å20 Å2
2---2 Å20 Å2
3---5.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 236 1644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
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: 1.8→1.91 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.232 3930 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCNS_PROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

+
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://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