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- PDB-7csp: Structure of Ephexin4 IDPSH -

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Basic information

Entry
Database: PDB / ID: 7csp
TitleStructure of Ephexin4 IDPSH
ComponentsRho guanine nucleotide exchange factor 16
KeywordsSIGNALING PROTEIN / Ephexin4 / GEF / Autoinhibition
Function / homology
Function and homology information


CDC42 GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / activation of GTPase activity / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / positive regulation of protein localization to plasma membrane / receptor tyrosine kinase binding ...CDC42 GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / activation of GTPase activity / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / positive regulation of protein localization to plasma membrane / receptor tyrosine kinase binding / small GTPase binding / cytoplasm
Similarity search - Function
ARHGEF16/ARHGEF26, SH3 domain / Variant SH3 domain / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. ...ARHGEF16/ARHGEF26, SH3 domain / Variant SH3 domain / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 16
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, M. / Lin, L. / Wang, C. / Zhu, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Double inhibition and activation mechanisms of Ephexin family RhoGEFs.
Authors: Zhang, M. / Lin, L. / Wang, C. / Zhu, J.
History
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 16
B: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)114,9142
Polymers114,9142
Non-polymers00
Water0
1
A: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)57,4571
Polymers57,4571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)57,4571
Polymers57,4571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.082, 143.082, 138.543
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 264 through 709)
21(chain B and (resid 264 through 516 or resid 528 through 571 or resid 583 through 709))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 264 through 709)A264 - 709
211(chain B and (resid 264 through 516 or resid 528 through 571 or resid 583 through 709))B264 - 516
221(chain B and (resid 264 through 516 or resid 528 through 571 or resid 583 through 709))B528 - 571
231(chain B and (resid 264 through 516 or resid 528 through 571 or resid 583 through 709))B583 - 709

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Components

#1: Protein Rho guanine nucleotide exchange factor 16 / Ephexin-4


Mass: 57456.906 Da / Num. of mol.: 2 / Mutation: 242-252 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgef16 / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): BL21(DE3) / References: UniProt: Q3U5C8

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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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium acetate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→46.83 Å / Num. obs: 59938 / % possible obs: 94.8 % / Redundancy: 3.688 % / Biso Wilson estimate: 80.826 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Χ2: 0.867 / Net I/σ(I): 10.35 / Num. measured all: 221044
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.193.5310.9551.27334221020494650.4761.12392.8
3.19-3.43.7330.4762.7133733957190370.8070.55494.4
3.4-3.683.8590.2365.4132885892785220.9450.27495.5
3.68-4.023.7880.1269.3929638818378250.9820.14795.6
4.02-4.53.6360.08213.8225825745571020.990.09695.3
4.5-5.183.5520.06217.9422093657462200.9930.07294.6
5.18-6.333.8390.06218.3520374553453070.9940.07295.9
6.33-8.873.540.04922.2214685432341480.9960.05896
8.87-46.833.6280.04228.058389245523120.9960.04894.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CSO
Resolution: 3→46.83 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1958 6.32 %
Rwork0.1847 29036 -
obs0.1877 30994 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.02 Å2 / Biso mean: 88.2665 Å2 / Biso min: 36.69 Å2
Refinement stepCycle: final / Resolution: 3→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7349 0 0 0 7349
Num. residues----903
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2578X-RAY DIFFRACTION6.087TORSIONAL
12B2578X-RAY DIFFRACTION6.087TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.080.36841280.33661903203189
3.08-3.160.3811340.29071982211693
3.16-3.260.33411270.27512028215594
3.26-3.360.32951400.25272054219496
3.36-3.480.29831430.23652074221797
3.48-3.620.26131410.20512081222298
3.62-3.790.22731390.18262115225498
3.79-3.980.22421350.1862124225998
3.98-4.230.2361400.17092097223799
4.23-4.560.21651430.16272111225498
4.56-5.020.1761410.15162115225698
5.02-5.740.23851450.17782126227198
5.75-7.230.24821530.19772116226999
7.24-46.830.16591490.14232110225996

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