[English] 日本語
Yorodumi
- PDB-7g97: ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7g97
TitleARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z57899718
Components
  • Rho guanine nucleotide exchange factor 2
  • Transforming protein RhoA
KeywordsCYTOSOLIC PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 / cellular response to muramyl dipeptide / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / positive regulation of neuron migration / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / negative regulation of microtubule depolymerization / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / regulation of Rho protein signal transduction / cellular hyperosmotic response / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of necroptotic process / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / regulation of small GTPase mediated signal transduction / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / PI3K/AKT activation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / RHOB GTPase cycle / myosin binding / NRAGE signals death through JNK / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cellular response to cytokine stimulus / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / bicellular tight junction / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / secretory granule membrane
Similarity search - Function
ARHGEF2, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family 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. ...ARHGEF2, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-AMINOMETHYL-PYRIDINE / FORMIC ACID / Transforming protein RhoA / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.3 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: ARHGEF2 PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionJun 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming protein RhoA
B: Rho guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9597
Polymers49,5702
Non-polymers3895
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-2 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.226, 71.226, 196.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-648-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Transforming protein RhoA / / Rho cDNA clone 12 / h12


Mass: 20925.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586, small monomeric GTPase
#2: Protein Rho guanine nucleotide exchange factor 2 / Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell ...Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell nucleolar antigen p40


Mass: 28644.150 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92974

-
Non-polymers , 4 types, 92 molecules

#3: Chemical ChemComp-APY / 2-AMINOMETHYL-PYRIDINE / 2-Picolylamine


Mass: 108.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris, 2.6M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.3→71.27 Å / Num. obs: 23427 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.992 / Rmerge(I) obs: 0.636 / Rpim(I) all: 0.143 / Rrim(I) all: 0.666 / Net I/σ(I): 6.1 / Num. measured all: 491371 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.3-2.3821.45.2824795822370.6291.185.4981.3
8.91-71.2715.50.08278655060.9980.0210.08616.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0405refinement
Aimless0.7.9data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BNT

8bnt


Resolution: 2.3→66.94 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.687 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1158 5 %RANDOM
Rwork0.1898 ---
obs0.1928 22169 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.91 Å2 / Biso mean: 36.521 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å20 Å2
2--1.15 Å20 Å2
3----2.3 Å2
Refinement stepCycle: final / Resolution: 2.3→66.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 23 87 3450
Biso mean--52 31.76 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123421
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163325
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6534602
X-RAY DIFFRACTIONr_angle_other_deg0.5161.5767663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.653529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16110647
X-RAY DIFFRACTIONr_chiral_restr0.0720.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
X-RAY DIFFRACTIONr_mcbond_it3.4753.3221654
X-RAY DIFFRACTIONr_mcbond_other3.4753.3241655
X-RAY DIFFRACTIONr_mcangle_it5.4085.9592064
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 79 -
Rwork0.267 1582 -
all-1661 -
obs--99.88 %

+
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