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- PDB-4dvg: Crystal structure of E. histolytica Formin1 bound to EhRho1-GTPgammaS -

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Basic information

Entry
Database: PDB / ID: 4dvg
TitleCrystal structure of E. histolytica Formin1 bound to EhRho1-GTPgammaS
Components
  • Diaphanous proteinTransparency and translucency
  • Rho-like small GTPase
KeywordsGTP binding/Actin binding Proteins / cytoskeleton / Armadillo repeat / GTPase-binding domain / nucleotide-binding / signaling protein / lipoprotein / actin filament formation / prenylation / GTP binding-Actin binding Proteins complex
Function / homology
Function and homology information


protein localization to phagocytic vesicle / small GTPase binding => GO:0031267 / adhesion of symbiont to host cell / small GTPase-mediated signal transduction / phagocytic cup / phagocytosis / positive regulation of phagocytosis / phagocytic vesicle / small monomeric GTPase / cell projection ...protein localization to phagocytic vesicle / small GTPase binding => GO:0031267 / adhesion of symbiont to host cell / small GTPase-mediated signal transduction / phagocytic cup / phagocytosis / positive regulation of phagocytosis / phagocytic vesicle / small monomeric GTPase / cell projection / actin binding / actin cytoskeleton organization / cytoskeleton / GTPase activity / GTP binding / protein kinase binding / magnesium ion binding / metal ion binding / cytosol
Similarity search - Function
Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily ...Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / small GTPase Rab1 family profile. / Small GTPase Rho / small GTPase Rho family profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / small GTPase Ras 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 / Armadillo-like helical / Alpha Horseshoe / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-like GTP-binding protein RHO1 / Diaphanous protein, putative / Rho-like small GTPase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: Biochemistry / Year: 2012
Title: Entamoeba histolytica Rho1 Regulates Actin Polymerization through a Divergent, Diaphanous-Related Formin.
Authors: Bosch, D.E. / Yang, B. / Siderovski, D.P.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-like small GTPase
B: Diaphanous protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6134
Polymers62,0502
Non-polymers5642
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.564, 138.564, 57.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Rho-like small GTPase


Mass: 20749.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhRho1 / Plasmid: pLIC-His / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q95TD4, UniProt: C4M4W4*PLUS, small monomeric GTPase
#2: Protein Diaphanous protein / Transparency and translucency


Mass: 41300.102 Da / Num. of mol.: 1 / Fragment: GBD-FH3, UNP residues 69-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhFormin1, EHI_125300 / Plasmid: pLIC-His / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: C4M622
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


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

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: EhRho1-GTPgammaS at 5 mg/mL and and EhFormin1 at 10 mg/mL were mixed in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GTPgammaS, 1 mM ...Details: EhRho1-GTPgammaS at 5 mg/mL and and EhFormin1 at 10 mg/mL were mixed in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GTPgammaS, 1 mM magnesium chloride) and allowed to form a complex for 30 minutes at room temperature. The protein solution was then mixed 1:1 and equilibrated against crystallization solution (18% PEG 3350, 100 mM Tris pH 8.5, 200 mM magnesium chloride)., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 22, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 19500 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.6→2.63 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.604→35.673 Å / SU ML: 0.92 / σ(F): 0 / Phase error: 27.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1938 10.09 %RANDOM
Rwork0.2152 ---
obs0.2188 19211 97.85 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.635 Å2 / ksol: 0.261 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0438 Å20 Å20 Å2
2---3.0438 Å2-0 Å2
3---6.0876 Å2
Refinement stepCycle: LAST / Resolution: 2.604→35.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 33 4 3784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013845
X-RAY DIFFRACTIONf_angle_d1.2335193
X-RAY DIFFRACTIONf_dihedral_angle_d14.6681446
X-RAY DIFFRACTIONf_chiral_restr0.079592
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.604-2.66870.37211210.33431092X-RAY DIFFRACTION86
2.6687-2.74080.3661320.34021164X-RAY DIFFRACTION94
2.7408-2.82150.35781320.31081186X-RAY DIFFRACTION96
2.8215-2.91250.33931420.29111235X-RAY DIFFRACTION98
2.9125-3.01650.31400.2691232X-RAY DIFFRACTION98
3.0165-3.13720.28961370.24731230X-RAY DIFFRACTION99
3.1372-3.27990.31441360.24891254X-RAY DIFFRACTION100
3.2799-3.45270.32851420.2481260X-RAY DIFFRACTION100
3.4527-3.66880.2731370.2341253X-RAY DIFFRACTION100
3.6688-3.95180.22321420.20081261X-RAY DIFFRACTION100
3.9518-4.34880.21021420.17451257X-RAY DIFFRACTION100
4.3488-4.97670.191390.15731275X-RAY DIFFRACTION100
4.9767-6.26450.21121500.20881278X-RAY DIFFRACTION100
6.2645-35.67670.2441460.20271296X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.5973-5.024.33682.1664-4.64142.1894-0.41021.0356-0.09180.1705-0.3075-1.094-1.480.88850.80220.8629-0.17470.01760.6144-0.05170.606547.563158.558316.0614
26.40124.62010.45884.16491.54442.8904-0.348-0.01380.82590.246-0.5846-1.3719-1.08930.59930.53490.8641-0.1501-0.2180.5897-0.01081.342753.10260.796314.4087
35.80994.02060.41467.7211.46593.7858-0.25920.16520.2768-0.5812-0.0697-1.2355-0.91830.71530.10730.8253-0.1423-0.10650.3766-0.20821.21350.348352.384618.4134
42.45240.25930.6072.9656-2.32533.10160.1091-0.1206-0.34770.47590.1666-0.3183-0.7196-0.0771-0.20810.77940.09790.08510.3484-0.10890.5740.271652.727522.3332
51.45030.182-1.44222.8147-4.00699.9337-0.06080.34870.19890.1295-0.22570.25-0.1822-0.81420.06041.04160.60750.05921.30460.13260.204327.537165.96815.3427
60.7117-1.1614-0.49991.88430.9813.82270.2150.18340.6612-0.0742-0.22450.124-1.3582-0.4955-0.04541.50640.83340.37070.6745-0.4319-0.199531.57359.87928.8079
74.3991-1.04941.70391.34570.83058.0452-0.1040.44560.155-0.1190.6409-0.1788-1.4377-0.8225-0.26091.49790.22690.07220.47390.04410.267540.949266.825919.0503
80.54270.78940.64351.86421.85791.8671-0.5009-0.86260.83860.5582-0.1308-0.968-1.02250.52270.19451.7282-0.514-0.54780.077-0.65050.672548.827265.95727.9675
97.66764.71190.74983.33370.95270.82940.4970.0289-0.24820.667-0.24650.02140.7260.5188-0.06250.99640.28680.34840.9977-0.13441.423258.918935.8813.2907
109.1202-2.9675-4.49298.0092-3.92382.023-0.97011.0420.1146-1.3218-0.439-1.47990.6913-1.4631.49641.20230.22720.2521.098-0.25591.159553.554140.82546.9174
115.53073.3371-1.46522.1665-1.67666.09021.0854-1.15530.51641.1005-0.9419-2.26960.30961.58740.07820.82870.0824-0.15190.96330.05771.40356.338539.179625.1203
121.9973-5.70537.38237.1177-8.84052.0061-0.2734-2.01530.87481.1962-0.8561-0.43-0.91330.18950.78321.7948-0.38480.18971.495-0.72871.531242.371236.167839.7738
135.59790.2141.44695.04412.17274.5484-0.0115-0.38360.22110.797-0.0278-0.10910.348-0.27330.04560.47870.04740.09130.35050.0170.535731.060929.406523.2258
141.6498-1.05450.14224.4061-0.74143.71910.00740.1613-0.2136-0.42110.3594-0.42970.49480.3261-0.25070.4502-0.00120.02770.3643-0.12550.699530.258520.11668.6772
150.7864-0.37573.01675.27043.59471.99660.6701-0.64480.4942-0.2643-0.02830.6218-1.257-1.9496-0.68410.755-0.2280.17651.04960.02010.541810.537218.746710.3539
162.41140.12942.08813.38323.27154.88560.02780.2030.5032-1.4480.1169-0.4497-0.83540.0824-0.15330.71210.03470.17340.41420.11790.620621.112223.0165-6.7859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 21:42)
2X-RAY DIFFRACTION2(chain A and resid 43:65)
3X-RAY DIFFRACTION3(chain A and resid 66:83)
4X-RAY DIFFRACTION4(chain A and resid 84:135)
5X-RAY DIFFRACTION5(chain A and resid 136:147)
6X-RAY DIFFRACTION6(chain A and resid 148:157)
7X-RAY DIFFRACTION7(chain A and resid 158:172)
8X-RAY DIFFRACTION8(chain A and resid 173:184)
9X-RAY DIFFRACTION9(chain B and resid 73:86)
10X-RAY DIFFRACTION10(chain B and resid 87:96)
11X-RAY DIFFRACTION11(chain B and resid 97:119)
12X-RAY DIFFRACTION12(chain B and resid 120:127)
13X-RAY DIFFRACTION13(chain B and resid 128:236)
14X-RAY DIFFRACTION14(chain B and resid 237:279)
15X-RAY DIFFRACTION15(chain B and resid 280:285)
16X-RAY DIFFRACTION16(chain B and resid 286:377)

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