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- PDB-6x1g: Crystal structure of a GEF domain from the Orientia tsutsugamushi... -

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Basic information

Entry
Database: PDB / ID: 6x1g
TitleCrystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1
Components
  • Ras-related C3 botulinum toxin substrate 1
  • ULP_PROTEASE domain-containing protein
KeywordsSIGNALING PROTEIN/HYDROLASE / guanine nucleotide exchange factor / GEF / Rac1 / GTPase / Orientia tsutsugamushi / scrub typhus / SIGNALING PROTEIN / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / cysteine-type peptidase activity / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / response to wounding / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer
Similarity search - Function
Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / 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 / Papain-like cysteine peptidase superfamily ...Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / 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 / Papain-like cysteine peptidase superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ubiquitin-like protease family profile domain-containing protein / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesOrientia tsutsugamushi (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLim, C.S. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE1122492 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi .
Authors: Lim, C. / Berk, J.M. / Blaise, A. / Bircher, J. / Koleske, A.J. / Hochstrasser, M. / Xiong, Y.
History
DepositionMay 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein
C: ULP_PROTEASE domain-containing protein
B: Ras-related C3 botulinum toxin substrate 1
D: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4855
Polymers91,4604
Non-polymers241
Water5,603311
1
A: ULP_PROTEASE domain-containing protein
B: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)45,7302
Polymers45,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-15 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: ULP_PROTEASE domain-containing protein
D: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7543
Polymers45,7302
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-19 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.063, 54.160, 94.004
Angle α, β, γ (deg.)83.370, 76.340, 62.520
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA547 - 7621 - 216
21CB547 - 7621 - 216
12BC1 - 1781 - 178
22DD1 - 1781 - 178

NCS ensembles :
ID
1
2

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Components

#1: Protein ULP_PROTEASE domain-containing protein


Mass: 25190.531 Da / Num. of mol.: 2 / Fragment: GEF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orientia tsutsugamushi (bacteria) / Strain: Ikeda / Gene: OTT_1962 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CVM3
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Rac1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20539.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 9.5 / Details: 25 mM CHES pH 9.5, 25% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 92107 / % possible obs: 81.7 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.038 / Rrim(I) all: 0.053 / Χ2: 1.348 / Net I/σ(I): 10.4 / Num. measured all: 151064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.631.60.73145100.2950.7311.0331.09180.2
1.63-1.661.60.66644370.350.6660.9421.0678.9
1.66-1.691.60.62245760.3980.6220.881.05780.8
1.69-1.721.60.52744490.5240.5270.7460.98879.2
1.72-1.761.60.41345120.6380.4130.5840.99880.1
1.76-1.81.60.38942680.6830.3890.551.01375.3
1.8-1.851.60.29742150.8020.2970.4210.99775
1.85-1.91.60.23447400.870.2340.3311.06784.6
1.9-1.951.60.18147240.9130.1810.2551.09183.5
1.95-2.021.70.13946520.9510.1390.1971.06582.2
2.02-2.091.70.10746220.9710.1070.1511.22581.5
2.09-2.171.60.08943160.9780.0890.1261.2676.8
2.17-2.271.70.07646140.9120.0760.1081.56682.1
2.27-2.391.70.05748770.990.0570.081.46386.7
2.39-2.541.70.05248350.990.0520.0731.55486
2.54-2.741.70.04546730.9910.0450.0641.67782.8
2.74-3.011.70.03946170.9930.0390.0551.87581.7
3.01-3.451.70.03249420.9950.0320.0451.86987.8
3.45-4.341.70.02945930.9960.0290.0411.97981.5
4.34-501.70.02549350.9960.0250.0351.49587.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOE

1foe


Resolution: 1.6→48.05 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.743 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 4663 5.1 %RANDOM
Rwork0.181 ---
obs0.1828 87425 81.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.29 Å2 / Biso mean: 45.588 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.29 Å2-0.22 Å2
2---0.37 Å2-0.05 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 1.6→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 1 311 6578
Biso mean--66.92 39.74 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176042
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.6398616
X-RAY DIFFRACTIONr_angle_other_deg1.5171.58214084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41423.827324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.429151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4821530
X-RAY DIFFRACTIONr_chiral_restr0.1010.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A6976
12C6976
21B5654
22D5654
LS refinement shellResolution: 1.6→1.638 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.388 318 -
Rwork0.368 6162 -
obs--77.73 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2043-0.59960.09361.1698-0.03190.9931-0.0163-0.0570.15740.1722-0.0253-0.0803-0.06260.02750.04160.0583-0.0345-0.00370.0974-0.0050.037721.10826.98445.848
21.01510.38740.00241.07210.00950.85380.02230.0548-0.1322-0.1463-0.0243-0.03850.05290.00820.0020.05750.01370.00510.1012-0.00850.0265-3.943.601-14.25
30.3790.0554-0.12880.71940.5171.7851-0.02190.01820.0094-0.0829-0.0452-0.03150.12010.00790.06710.0644-0.01120.02230.09960.01930.027819.72516.19225.161
40.4997-0.14230.13250.68320.47831.7136-0.0132-0.0190.00270.0876-0.032-0.0434-0.1136-0.00340.04520.0657-0.0086-0.00950.10040.01370.0237-5.27814.4386.336
50.08540.01640.11470.0560.08270.24390.0007-0.00480.0161-0.0038-0.03450.009-0.0074-0.01980.03390.0397-0.00930.00590.05520.00060.00644.17114.36813.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A547 - 762
2X-RAY DIFFRACTION2C548 - 762
3X-RAY DIFFRACTION3B1 - 178
4X-RAY DIFFRACTION4D1 - 178
5X-RAY DIFFRACTION5A801 - 871
6X-RAY DIFFRACTION5B202 - 274
7X-RAY DIFFRACTION5C901 - 987
8X-RAY DIFFRACTION5D202 - 278

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