[English] 日本語
Yorodumi
- PDB-1fhw: Structure of the pleckstrin homology domain from GRP1 in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fhw
TitleStructure of the pleckstrin homology domain from GRP1 in complex with inositol(1,3,4,5,6)pentakisphosphate
ComponentsGUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
KeywordsSIGNALING PROTEIN / PLECKSTRIN / 3-PHOSPHOINOSITIDES / INOSITOL TETRAKISPHOSPHATE SIGNAL TRANSDUCTION PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR
Function / homology
Function and homology information


Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / bicellular tight junction / ruffle / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction ...Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / bicellular tight junction / ruffle / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE / : / Cytohesin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsFerguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
CitationJournal: Mol.Cell / Year: 2000
Title: Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains
Authors: Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6955
Polymers30,4392
Non-polymers1,2563
Water2,954164
1
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7992
Polymers15,2191
Non-polymers5801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,2191
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-60 kcal/mol
Surface area12660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.970, 72.220, 46.900
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer constructed from chain A or chain B

-
Components

#1: Protein GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1 / GRP1


Mass: 15219.406 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH INOSITOL (1,3,4,5,6)-PENTAKISPHOSPHATE
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: GenBank: 2183209, UniProt: O08967*PLUS
#2: Chemical ChemComp-I5P / INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE


Mass: 580.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17O21P5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 29.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-10 %PEG80001reservoir
250 mMsodium acetate1reservoir
3200 mMammonium sulfate1reservoir
415 mg/mlprotein1drop
510 mMMES1drop
6100 mM1dropNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 53932 / Num. obs: 18374 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 10.7 / Rsym value: 0.08 / % possible all: 80.5
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Num. measured all: 53932
Reflection shell
*PLUS
% possible obs: 80.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→46.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1114520.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1795 9.8 %RANDOM
Rwork0.229 ---
all0.229 18358 --
obs0.229 18358 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.34 Å20 Å2-8.01 Å2
2---5.66 Å20 Å2
3----3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 69 164 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it2.882
X-RAY DIFFRACTIONc_scbond_it2.652
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 225 10.2 %
Rwork0.229 1972 -
obs--66.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM.IP5TOP.IP5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.229

+
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