[English] 日本語
Yorodumi
- PDB-6bnm: Crystal Structure of the P-Rex2 PH domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bnm
TitleCrystal Structure of the P-Rex2 PH domain
ComponentsPhosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein
KeywordsLIPID BINDING PROTEIN / pleckstrin homology domain / beta sandwich / phosphatidylinositol-binding
Function / homology
Function and homology information


: / dendrite morphogenesis / adult locomotory behavior / GTPase activator activity / guanyl-nucleotide exchange factor activity / Regulation of PTEN stability and activity / G protein-coupled receptor signaling pathway / plasma membrane / cytosol
Similarity search - Function
PREX2, DEP domain 1 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases ...PREX2, DEP domain 1 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCash, J.N. / Sharma, P.V. / Tesmer, J.J.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
American Cancer Society-Michigan Cancer Research FundPF-14-224-01-DMC United States
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural and biochemical characterization of the pleckstrin homology domain of the RhoGEF P-Rex2 and its regulation by PIP3.
Authors: Cash, J.N. / Sharma, P.V. / Tesmer, J.J.G.
History
DepositionNov 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2095
Polymers19,0671
Non-polymers1424
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-36 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.105, 60.105, 86.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein / PtdIns(3 / 4 / 5)-dependent Rac exchanger 2 / DEP domain-containing protein 2


Mass: 19066.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREX2, DEPDC2 / Plasmid: pMALc2H10T
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q70Z35
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Sodium Acetate pH 5, 3.325 M Sodium Chloride

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.9→52.05 Å / Num. obs: 14598 / % possible obs: 99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.024 / Rrim(I) all: 0.069 / Χ2: 1.027 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.50.7137000.7260.350.7990.57696.8
1.93-1.9750.6377150.8240.2920.7040.5999.9
1.97-2.015.70.4947340.8890.2130.540.637100
2.01-2.057.30.4027060.9320.1560.4320.662100
2.05-2.097.60.3457190.9510.1320.370.68999.9
2.09-2.147.70.2697430.9660.1020.2880.799.9
2.14-2.197.50.2147130.9740.0820.230.73899.9
2.19-2.257.60.187350.9860.0680.1930.7799.9
2.25-2.327.80.1647350.9870.0610.1750.79899.9
2.32-2.397.60.1297130.9890.0490.1390.78699.7
2.39-2.487.70.1247230.9930.0460.1330.89799.2
2.48-2.587.60.1067270.9930.040.1141.03899.6
2.58-2.77.60.1037360.9940.0390.1111.3199.3
2.7-2.847.60.0897300.9960.0330.0951.60499.5
2.84-3.027.70.077360.9970.0250.0741.6399.2
3.02-3.257.60.0527230.9980.0190.0551.35298.9
3.25-3.587.70.0497410.9980.0180.0521.18998.5
3.58-4.097.60.0567380.9970.020.0591.49198
4.09-5.167.60.0387430.9990.0140.041.33697.1
5.16-507.10.0367880.9990.0140.0391.17995.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.17 Å44.56 Å
Translation5.17 Å44.56 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SCALEPACK2.5.7data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D27

5d27


Resolution: 1.9→52.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.413 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 736 5 %RANDOM
Rwork0.1908 ---
obs0.1928 13861 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.23 Å2 / Biso mean: 36.253 Å2 / Biso min: 19.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.22 Å20 Å2
2---0.43 Å20 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 1.9→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 4 74 1213
Biso mean--34.62 40.6 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191160
X-RAY DIFFRACTIONr_bond_other_d0.0020.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9171557
X-RAY DIFFRACTIONr_angle_other_deg0.91132506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69724.03262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63115217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.798158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
LS refinement shellResolution: 1.899→1.948 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 64 -
Rwork0.286 981 -
all-1045 -
obs--97.21 %

+
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