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- PDB-8etd: Crystal Structure of Schizosaccharomyces pombe Rho1 -

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Basic information

Entry
Database: PDB / ID: 8etd
TitleCrystal Structure of Schizosaccharomyces pombe Rho1
ComponentsGTP-binding protein rho1
KeywordsGENE REGULATION / GTPase / Rho / GDP / Evolution
Function / homology
Function and homology information


positive regulation of (1->3)-beta-D-glucan biosynthetic process / regulation of fungal-type cell wall (1->3)-alpha-glucan biosynthetic process / positive regulation of regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process / positive regulation of primary cell septum biogenesis / regulation of establishment or maintenance of cell polarity regulating cell shape / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events / RHO GTPases activate PKNs / RHOF GTPase cycle ...positive regulation of (1->3)-beta-D-glucan biosynthetic process / regulation of fungal-type cell wall (1->3)-alpha-glucan biosynthetic process / positive regulation of regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process / positive regulation of primary cell septum biogenesis / regulation of establishment or maintenance of cell polarity regulating cell shape / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events / RHO GTPases activate PKNs / RHOF GTPase cycle / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / positive regulation of mitotic division septum assembly / cell cortex of growing cell tip / RHOD GTPase cycle / protein aggregate center / regulation of cell wall (1->3)-beta-D-glucan biosynthetic process / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / growing cell tip / regulation of fungal-type cell wall biogenesis / regulation of division septum assembly / Neutrophil degranulation / medial cortex / division septum / small GTPase-mediated signal transduction / regulation of endocytosis / signaling adaptor activity / actin filament organization / regulation of actin cytoskeleton organization / cytoplasmic side of plasma membrane / GDP binding / GTPase activity / protein kinase binding / GTP binding / signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein rho1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsHuang, Q. / Xie, J. / Seetharaman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other government Singapore
CitationJournal: Biology (Basel) / Year: 2022
Title: Crystal Structure of Schizosaccharomyces pombe Rho1 Reveals Its Evolutionary Relationship with Other Rho GTPases.
Authors: Huang, Q. / Xie, J. / Seetharaman, J.
History
DepositionOct 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: GTP-binding protein rho1
B: GTP-binding protein rho1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0456
Polymers45,1102
Non-polymers9354
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.691, 66.349, 75.551
Angle α, β, γ (deg.)90.000, 112.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GTP-binding protein rho1


Mass: 22555.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rho1, SPAC1F7.04 / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q09914
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic tetrahydrate (pH 5.6), 1.9 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 12478 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.2
Reflection shellResolution: 2.78→2.83 Å / Rmerge(I) obs: 0.82 / Num. unique obs: 617 / CC1/2: 0.514

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zvp

5zvp


Resolution: 2.78→39.14 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 604 4.92 %
Rwork0.1912 11679 -
obs0.1932 12283 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.02 Å2 / Biso mean: 23.7813 Å2 / Biso min: 3.79 Å2
Refinement stepCycle: final / Resolution: 2.78→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 58 128 2932
Biso mean--14.95 22.63 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.78-3.060.27991640.236428833047
3.06-3.50.24941440.205729143058
3.5-4.410.22051610.170328943055
4.41-39.140.20281350.178229883123

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