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- PDB-9j0g: Crystal structure of RhoA-TP1001 complex -

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Basic information

Entry
Database: PDB / ID: 9j0g
TitleCrystal structure of RhoA-TP1001 complex
ComponentsTransforming protein RhoA
KeywordsSIGNALING PROTEIN / Complex
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 / regulation of modification of postsynaptic structure / cell junction assembly / apical 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 oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / stress fiber assembly / androgen receptor signaling pathway / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / skeletal muscle tissue development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / Rho protein signal transduction / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of cell migration / regulation of microtubule cytoskeleton organization / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / neuron migration / cell morphogenesis / Ovarian tumor domain proteases / cell junction / G beta:gamma signalling through PI3Kgamma
Similarity search - Function
Small GTPase Rho / Small GTPase Rho domain 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 / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhu, L. / Li, H. / Chang, L. / Hu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82150208 China
CitationJournal: To Be Published
Title: Crystal structure of RhoA-TP1001 complex
Authors: Zhu, L. / Li, H. / Chang, L. / Hu, X.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Transforming protein RhoA
C: Transforming protein RhoA
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,38816
Polymers87,0644
Non-polymers2,32312
Water724
1
A: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2343
Polymers21,7661
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2584
Polymers21,7661
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2343
Polymers21,7661
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6626
Polymers21,7661
Non-polymers8965
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.240, 124.800, 173.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 21766.088 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 16 molecules

#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-U6L / (1~{R})-1-(3-ethylphenyl)ethane-1,2-diol / SCHEMBL24015313


Mass: 166.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.5 M Lithium sulfate monohydrate,0.1 M HEPES pH 7.5,30% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.1→44.12 Å / Num. obs: 16388 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.987 / Net I/σ(I): 10.6
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.439 / Num. unique obs: 2906 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-30007.21data scaling
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTN

1ftn


Resolution: 3.1→44.08 Å / Cor.coef. Fo:Fc: 0.803 / Cor.coef. Fo:Fc free: 0.724 / SU B: 35.051 / SU ML: 0.637 / Cross valid method: THROUGHOUT / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3541 849 5.2 %RANDOM
Rwork0.31065 ---
obs0.31298 15513 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2--0.15 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 3.1→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 145 4 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125847
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165560
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.8517931
X-RAY DIFFRACTIONr_angle_other_deg0.5631.78612873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4765700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.13540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91101034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021232
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_it2.13.3062821
X-RAY DIFFRACTIONr_mcbond_other2.13.3062821
X-RAY DIFFRACTIONr_mcangle_it3.5695.9423514
X-RAY DIFFRACTIONr_mcangle_other3.5695.9413515
X-RAY DIFFRACTIONr_scbond_it1.7963.4223026
X-RAY DIFFRACTIONr_scbond_other1.7933.4213024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0766.2584418
X-RAY DIFFRACTIONr_long_range_B_refined6.1433.266725
X-RAY DIFFRACTIONr_long_range_B_other6.1433.266726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 56 -
Rwork0.315 1112 -
obs--99.66 %

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