[English] 日本語
Yorodumi
- PDB-5fr2: Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fr2
TitleFarnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetylated at K178
Components
  • RHO GDP-DISSOCIATION INHIBITOR 1
  • TRANSFORMING PROTEIN RHOA
KeywordsSIGNALING PROTEIN / LYSINE-ACETYLATION / RHOA / RAS-SUPERFAMILY / RHOGDI / CYTOSKELETON / GDP
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / 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 ...Rho GDP-dissociation inhibitor activity / 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 / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / 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 / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / immunological synapse / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / regulation of cell migration / 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 / GTPase activator activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / FARNESYL / GUANOSINE-5'-DIPHOSPHATE / Rho GDP-dissociation inhibitor 1 / Transforming protein RhoA
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsKuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. ...Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Mechanistic Insights Into the Regulation of the Fundamental Rho-Regulator Rhogdi Alpha by Lysine Acetylation.
Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / ...Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M.
History
DepositionDec 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSFORMING PROTEIN RHOA
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4616
Polymers46,6072
Non-polymers8544
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-33.3 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.979, 176.979, 63.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein TRANSFORMING PROTEIN RHOA / / RHO CDNA CLONE 12 / H12 / RHOA


Mass: 21943.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIOESTER BETWEEN CYS190 AND FARNESYL-MOIETY / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein RHO GDP-DISSOCIATION INHIBITOR 1 / RHO GDI 1 / RHO-GDI ALPHA / RHOGDI-ALPHA


Mass: 24663.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LYSINE-ACETYLATED AT K178 / Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PCDF-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19803

-
Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 20 molecules

#3: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.09 Å3/Da / Density % sol: 41.28 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUMSULFATE 0.1 M BIS-TRIS PH5.5 25% PEG3350 30% DEXTROSE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014 / Details: MIRRORS
RadiationMonochromator: BARTELS SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→44.24 Å / Num. obs: 17709 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Biso Wilson estimate: 46.52 Å2 / Rmerge(I) obs: 0.52 / Net I/σ(I): 7.1
Reflection shellResolution: 3.35→3.62 Å / Redundancy: 15.7 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOA

1doa


Resolution: 3.35→44.245 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 838 5 %
Rwork0.2362 --
obs0.2374 16696 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.17 Å2
Refinement stepCycle: LAST / Resolution: 3.35→44.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 56 17 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033027
X-RAY DIFFRACTIONf_angle_d0.7864086
X-RAY DIFFRACTIONf_dihedral_angle_d16.031162
X-RAY DIFFRACTIONf_chiral_restr0.027451
X-RAY DIFFRACTIONf_plane_restr0.003520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3508-3.56070.28671390.2692585X-RAY DIFFRACTION99
3.5607-3.83550.29371480.25322611X-RAY DIFFRACTION100
3.8355-4.22130.23911170.22332626X-RAY DIFFRACTION100
4.2213-4.83170.2311290.21362641X-RAY DIFFRACTION100
4.8317-6.08560.25641510.23042646X-RAY DIFFRACTION100
6.0856-49.07120.29291510.25842706X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 67.9201 Å / Origin y: -55.5152 Å / Origin z: -19.6459 Å
111213212223313233
T0.1926 Å20.0061 Å2-0.001 Å2-0.3348 Å2-0.0346 Å2--0.1856 Å2
L2.771 °21.3544 °20.2588 °2-2.1624 °20.1937 °2--1.0936 °2
S0.0643 Å °-0.0324 Å °0.0913 Å °-0.0095 Å °-0.0268 Å °0.1689 Å °-0.0759 Å °-0.2204 Å °-0.0038 Å °
Refinement TLS groupSelection details: ALL

+
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