[English] 日本語
Yorodumi
- PDB-3t06: Crystal Structure of the DH/PH fragment of PDZRHOGEF with N-termi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t06
TitleCrystal Structure of the DH/PH fragment of PDZRHOGEF with N-terminal regulatory elements in complex with Human RhoA
Components
  • Rho guanine nucleotide exchange factor 11
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / DH-PH RhoA complex / PDZRhoGEF / GUANINE NUCLEOTIDE EXCHANGE FACTOR / RhoA
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / PI3K/AKT activation / motor neuron apoptotic process / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / RHOB GTPase cycle / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / myosin binding / regulation of neuron projection development / establishment of cell polarity / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / striated muscle contraction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / GTPase activator activity / regulation of cell migration / guanyl-nucleotide exchange factor activity / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / regulation of actin cytoskeleton organization / regulation of cell growth
Similarity search - Function
Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS domain / RGS domain profile. ...Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Small GTPase Rho / Small GTPase Rho domain profile. / 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 profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Domain present in PSD-95, Dlg, and ZO-1/2. / Ras subfamily of RAS small GTPases / PDZ domain / Small GTPase / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 11 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBielnicki, J.A. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Insights into the Molecular Activation Mechanism of the RhoA-specific Guanine Nucleotide Exchange Factor, PDZRhoGEF.
Authors: Bielnicki, J.A. / Shkumatov, A.V. / Derewenda, U. / Somlyo, A.V. / Svergun, D.I. / Derewenda, Z.S.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)137,2484
Polymers137,2484
Non-polymers00
Water00
1
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)68,6242
Polymers68,6242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-6 kcal/mol
Surface area25610 Å2
MethodPISA
2
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)68,6242
Polymers68,6242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-6 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 118.630, 92.443
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Rho guanine nucleotide exchange factor 11 / PDZ-RhoGEF


Mass: 48462.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pDEST15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15085
#2: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20161.037 Da / Num. of mol.: 2 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARH12, ARHA, RHO12, RHOA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-malic acid, 20 % w/v PEG 3350, pH 7.0, vapor diffusion, sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 12.02 / Number: 135276 / Rmerge(I) obs: 0.097 / Χ2: 1.01 / D res high: 2.84 Å / D res low: 30 Å / Num. obs: 36903 / % possible obs: 93.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.693099.710.0590.9953.8
6.127.6910010.071.0463.9
5.366.1299.910.0780.983.9
4.875.3610010.0721.0073.9
4.524.8710010.0681.0474
4.254.5210010.0741.0614
4.044.2510010.0820.9464
3.874.0410010.0941.0064
3.723.8799.910.1111.0574
3.593.7299.910.1311.0864
3.483.5999.810.1671.0444
3.383.4810010.1991.0753.9
3.293.3899.710.2520.9563.9
3.213.2999.210.2950.9613.7
3.143.2196.910.3180.9963.4
3.073.1491.710.330.9983.2
3.013.0783.610.3490.9933
2.953.0175.710.3890.9722.7
2.92.9567.810.3931.0012.5
2.852.959.110.3960.952.3
ReflectionResolution: 2.84→30 Å / Num. all: 39384 / Num. obs: 36903 / % possible obs: 93.7 % / Observed criterion σ(I): -4 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.84-2.92.30.396159.1
2.9-2.952.50.393167.8
2.95-3.012.70.389175.7
3.01-3.0730.349183.6
3.07-3.143.20.33191.7
3.14-3.213.40.318196.9
3.21-3.293.70.295199.2
3.29-3.383.90.252199.7
3.38-3.483.90.1991100
3.48-3.5940.167199.8
3.59-3.7240.131199.9
3.72-3.8740.111199.9
3.87-4.0440.0941100
4.04-4.2540.0821100
4.25-4.5240.0741100
4.52-4.8740.0681100
4.87-5.363.90.0721100
5.36-6.123.90.078199.9
6.12-7.693.90.071100
7.69-303.80.059199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_818refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XCG

1xcg


Resolution: 2.84→29.824 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.9 / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 1849 5.01 %
Rwork0.2077 --
obs0.2102 36871 93.55 %
all-39434 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.425 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.465 Å20 Å2-12.3514 Å2
2---11.4003 Å20 Å2
3----5.0647 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8657 0 0 0 8657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018802
X-RAY DIFFRACTIONf_angle_d1.26511870
X-RAY DIFFRACTIONf_dihedral_angle_d19.7843440
X-RAY DIFFRACTIONf_chiral_restr0.081345
X-RAY DIFFRACTIONf_plane_restr0.0051534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.9170.3543950.30521705X-RAY DIFFRACTION60
2.917-3.00270.39621170.29642129X-RAY DIFFRACTION74
3.0027-3.09960.31311380.28092461X-RAY DIFFRACTION87
3.0996-3.21020.3261620.25932754X-RAY DIFFRACTION96
3.2102-3.33860.36691430.25732856X-RAY DIFFRACTION99
3.3386-3.49030.30351590.23122866X-RAY DIFFRACTION100
3.4903-3.6740.2981380.22312890X-RAY DIFFRACTION100
3.674-3.90370.26541400.20492870X-RAY DIFFRACTION100
3.9037-4.20440.24771270.19842926X-RAY DIFFRACTION100
4.2044-4.62610.24111580.16882869X-RAY DIFFRACTION100
4.6261-5.29230.22381450.16792884X-RAY DIFFRACTION100
5.2923-6.65550.26081560.24172902X-RAY DIFFRACTION100
6.6555-29.82560.17571710.16962910X-RAY DIFFRACTION100

+
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