[English] 日本語
Yorodumi
- PDB-1u29: Triglycine variant of the ARNO Pleckstrin Homology Domain in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u29
TitleTriglycine variant of the ARNO Pleckstrin Homology Domain in complex with Ins(1,4,5)P3
ComponentsCytohesin 2
KeywordsLIPID BINDING PROTEIN / PH domain / lipid binding / phosphoinositide
Function / homology
Function and homology information


Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction / growth cone / postsynapse / lipid binding ...Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction / growth cone / postsynapse / lipid binding / glutamatergic synapse / plasma membrane / cytoplasm
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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Cytohesin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G.
CitationJournal: Embo J. / Year: 2004
Title: Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains
Authors: Cronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Cytohesin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4742
Polymers15,0541
Non-polymers4201
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.998, 56.378, 57.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cytohesin 2 / ARF nucleotide-binding site opener / ARNO protein / CLM2 / SEC7 homolog B / msec7-2


Mass: 15054.076 Da / Num. of mol.: 1 / Fragment: PH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pscd2, Sec7b / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63034
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, Hepes, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 13456 / Num. obs: 13437 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.85 Å / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FGY

1fgy


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.108 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. Several atoms for residues 287, 307, 318, 331, 333, 336, 343, 346, 362, 369, 376, 377, and 378 were modeled into this structure with zero ...Details: Hydrogens have been added in the riding positions. Several atoms for residues 287, 307, 318, 331, 333, 336, 343, 346, 362, 369, 376, 377, and 378 were modeled into this structure with zero occupancy because they are part of the PH domain and were not deleted or mutated.
RfactorNum. reflection% reflectionSelection details
Rfree0.26225 660 4.9 %RANDOM
Rwork0.22877 ---
all0.2304 12727 --
obs0.23038 12727 99.83 %-
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: 25.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---1.68 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 24 89 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021980
X-RAY DIFFRACTIONr_bond_other_d0.0020.02878
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9731338
X-RAY DIFFRACTIONr_angle_other_deg0.74832039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025118
X-RAY DIFFRACTIONr_chiral_restr0.0720.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021067
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02201
X-RAY DIFFRACTIONr_nbd_refined0.1770.2149
X-RAY DIFFRACTIONr_nbd_other0.2410.2933
X-RAY DIFFRACTIONr_nbtor_other0.080.2607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.27
X-RAY DIFFRACTIONr_mcbond_it0.7471.5593
X-RAY DIFFRACTIONr_mcangle_it1.42947
X-RAY DIFFRACTIONr_scbond_it1.9023387
X-RAY DIFFRACTIONr_scangle_it2.9194.5391
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 34
Rwork0.146 911

+
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