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- PDB-5zhx: Crystal structure of SmgGDS-558 and farnesylated RhoA complex -

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Basic information

Entry
Database: PDB / ID: 5zhx
TitleCrystal structure of SmgGDS-558 and farnesylated RhoA complex
Components
  • Rap1 GTPase-GDP dissociation stimulator 1
  • Transforming protein RhoA
KeywordsONCOPROTEIN / armadillo GEF chaperone
Function / homology
Function and homology information


regulation of ERK5 cascade / CAAX-box protein maturation / angiotensin-activated signaling pathway involved in heart process / RHOT1 GTPase cycle / RHOT2 GTPase cycle / regulation of matrix metallopeptidase secretion / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / negative regulation of endoplasmic reticulum calcium ion concentration ...regulation of ERK5 cascade / CAAX-box protein maturation / angiotensin-activated signaling pathway involved in heart process / RHOT1 GTPase cycle / RHOT2 GTPase cycle / regulation of matrix metallopeptidase secretion / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / negative regulation of endoplasmic reticulum calcium ion concentration / 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 / cardiac muscle hypertrophy / 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 / regulation of mitochondrion organization / 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 / negative regulation of GTPase activity / 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 / protein localization to nucleus / 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 / cell-matrix adhesion / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity
Similarity search - Function
Rap1 GTPase-GDP dissociation stimulator 1 / Small GTPase Rho / small GTPase Rho family profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Rap1 GTPase-GDP dissociation stimulator 1 / Small GTPase Rho / small GTPase Rho family profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FARNESYL / Rap1 GTPase-GDP dissociation stimulator 1 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsShimizu, H. / Toma-Fukai, S. / Shimizu, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism.
Authors: Shimizu, H. / Toma-Fukai, S. / Kontani, K. / Katada, T. / Shimizu, T.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rap1 GTPase-GDP dissociation stimulator 1
B: Rap1 GTPase-GDP dissociation stimulator 1
C: Rap1 GTPase-GDP dissociation stimulator 1
D: Rap1 GTPase-GDP dissociation stimulator 1
e: Transforming protein RhoA
f: Transforming protein RhoA
g: Transforming protein RhoA
h: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,17512
Polymers302,3508
Non-polymers8254
Water0
1
A: Rap1 GTPase-GDP dissociation stimulator 1
e: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7943
Polymers75,5872
Non-polymers2061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-11 kcal/mol
Surface area28780 Å2
MethodPISA
2
B: Rap1 GTPase-GDP dissociation stimulator 1
f: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7943
Polymers75,5872
Non-polymers2061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-17 kcal/mol
Surface area28830 Å2
MethodPISA
3
C: Rap1 GTPase-GDP dissociation stimulator 1
g: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7943
Polymers75,5872
Non-polymers2061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-15 kcal/mol
Surface area28700 Å2
MethodPISA
4
D: Rap1 GTPase-GDP dissociation stimulator 1
h: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7943
Polymers75,5872
Non-polymers2061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-14 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.320, 181.770, 205.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17e
27f
18e
28g
19e
29h
110f
210g
111f
211h
112g
212h

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A87 - 555
2010B87 - 555
1020A87 - 555
2020C87 - 555
1030A87 - 555
2030D87 - 555
1040B87 - 555
2040C87 - 555
1050B87 - 555
2050D87 - 555
1060C87 - 555
2060D87 - 555
1070e15 - 190
2070f3 - 182
1080e15 - 190
2080g3 - 182
1090e3 - 191
2090h3 - 191
10100f3 - 191
20100g3 - 191
10110f3 - 182
20110h15 - 190
10120g3 - 182
20120h15 - 190

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Rap1 GTPase-GDP dissociation stimulator 1 / Exchange factor smgGDS / SMG GDS protein / SMG P21 stimulatory GDP/GTP exchange protein


Mass: 53418.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1GDS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52306
#2: Protein
Transforming protein RhoA / / Rho cDNA clone 12 / h12


Mass: 22168.531 Da / Num. of mol.: 4 / Mutation: L193A
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
#3: Chemical
ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H26

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium malonate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→136.1 Å / Num. obs: 44892 / % possible obs: 99.9 % / Redundancy: 43.8 % / Biso Wilson estimate: 132.227 Å2 / Net I/σ(I): 10.4
Reflection shellResolution: 3.5→3.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 3.5→136.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30625 2213 5 %RANDOM
Rwork0.24994 ---
obs0.25278 42482 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0 Å2
2--0.13 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 3.5→136.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18728 0 0 0 18728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01918936
X-RAY DIFFRACTIONr_bond_other_d0.0040.0219096
X-RAY DIFFRACTIONr_angle_refined_deg1.421.97725608
X-RAY DIFFRACTIONr_angle_other_deg1.153343822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6952497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51225.78744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.881153362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0871584
X-RAY DIFFRACTIONr_chiral_restr0.0780.23096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221505
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023859
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.92913.23810038
X-RAY DIFFRACTIONr_mcbond_other6.92913.23810037
X-RAY DIFFRACTIONr_mcangle_it11.45119.84412516
X-RAY DIFFRACTIONr_mcangle_other11.4519.84412517
X-RAY DIFFRACTIONr_scbond_it6.99113.4578898
X-RAY DIFFRACTIONr_scbond_other6.99113.4578899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.80420.00813093
X-RAY DIFFRACTIONr_long_range_B_refined17.01120627
X-RAY DIFFRACTIONr_long_range_B_other17.01120628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A279800.09
12B279800.09
21A282950.08
22C282950.08
31A285130.07
32D285130.07
41B280110.09
42C280110.09
51B280650.09
52D280650.09
61C284700.07
62D284700.07
71e70990.16
72f70990.16
81e72030.15
82g72030.15
91e89850.14
92h89850.14
101f84930.12
102g84930.12
111f72960.13
112h72960.13
121g73200.13
122h73200.13
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 135 -
Rwork0.401 3148 -
obs--99.97 %

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