[English] 日本語
Yorodumi
- PDB-5zhx: Crystal structure of SmgGDS-558 and farnesylated RhoA complex -

+
Open data


ID or keywords:

Loading...

-
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


RHOT1 GTPase cycle / RHOT2 GTPase cycle / negative regulation of endoplasmic reticulum calcium ion concentration / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / CAAX-box protein maturation / alpha-beta T cell lineage commitment / aortic valve formation / beta selection ...RHOT1 GTPase cycle / RHOT2 GTPase cycle / negative regulation of endoplasmic reticulum calcium ion concentration / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / CAAX-box protein maturation / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / regulation of mitochondrion organization / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / ficolin-1-rich granule membrane / Rho protein signal transduction / RHOA GTPase cycle / protein localization to nucleus / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / GPVI-mediated activation cascade / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / guanyl-nucleotide exchange factor activity / secretory granule membrane / regulation of actin cytoskeleton organization / cell periphery / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium / cellular response to lipopolysaccharide / G alpha (12/13) signalling events / midbody / G protein activity
Similarity search - Function
Rap1 GTPase-GDP dissociation stimulator 1 / Small GTPase Rho / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Small GTPase Rho domain profile. / 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 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Small GTPase Rho domain profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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 (eV)
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:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTHRTHRAA87 - 55516 - 484
21ASPASPTHRTHRBB87 - 55516 - 484
12ASPASPTHRTHRAA87 - 55516 - 484
22ASPASPTHRTHRCC87 - 55516 - 484
13ASPASPTHRTHRAA87 - 55516 - 484
23ASPASPTHRTHRDD87 - 55516 - 484
14ASPASPTHRTHRBB87 - 55516 - 484
24ASPASPTHRTHRCC87 - 55516 - 484
15ASPASPTHRTHRBB87 - 55516 - 484
25ASPASPTHRTHRDD87 - 55516 - 484
16ASPASPTHRTHRCC87 - 55516 - 484
26ASPASPTHRTHRDD87 - 55516 - 484
17ALAALACYSCYSeE15 - 19020 - 195
27ALAALAARGARGfF3 - 1828 - 187
18ALAALACYSCYSeE15 - 19020 - 195
28ALAALAARGARGgG3 - 1828 - 187
19ALAALALEULEUeE3 - 1918 - 196
29ALAALALEULEUhH3 - 1918 - 196
110ALAALALEULEUfF3 - 1918 - 196
210ALAALALEULEUgG3 - 1918 - 196
111ALAALAARGARGfF3 - 1828 - 187
211ALAALACYSCYShH15 - 19020 - 195
112ALAALAARGARGgG3 - 1828 - 187
212ALAALACYSCYShH15 - 19020 - 195

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

-
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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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