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- PDB-7csr: Structure of Ephexin4 R676L -

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Basic information

Entry
Database: PDB / ID: 7csr
TitleStructure of Ephexin4 R676L
ComponentsRho guanine nucleotide exchange factor 16
KeywordsSIGNALING PROTEIN / Ephexin4 / GEF / Autoinhibition
Function / homology
Function and homology information


CDC42 GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOG GTPase cycle / activation of GTPase activity / guanyl-nucleotide exchange factor activity / cell chemotaxis / positive regulation of protein localization to plasma membrane / PDZ domain binding / receptor tyrosine kinase binding ...CDC42 GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOG GTPase cycle / activation of GTPase activity / guanyl-nucleotide exchange factor activity / cell chemotaxis / positive regulation of protein localization to plasma membrane / PDZ domain binding / receptor tyrosine kinase binding / small GTPase binding / cytoplasm
Similarity search - Function
ARHGEF16/ARHGEF26, SH3 domain / : / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. ...ARHGEF16/ARHGEF26, SH3 domain / : / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
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 17, 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
Revision 1.2Nov 29, 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: Rho guanine nucleotide exchange factor 16
B: Rho guanine nucleotide exchange factor 16
C: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)157,5653
Polymers157,5653
Non-polymers00
Water00
1
A: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)52,5221
Polymers52,5221
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)52,5221
Polymers52,5221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rho guanine nucleotide exchange factor 16


Theoretical massNumber of molelcules
Total (without water)52,5221
Polymers52,5221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.075, 244.729, 141.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 264 through 268 or (resid 269...
21(chain B and (resid 264 through 268 or (resid 269...
31(chain C and (resid 264 through 521 or (resid 522...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSER(chain A and (resid 264 through 268 or (resid 269...AA264 - 26810 - 14
12GLNGLNGLNGLN(chain A and (resid 264 through 268 or (resid 269...AA26915
13GLNGLNVALVAL(chain A and (resid 264 through 268 or (resid 269...AA264 - 70910 - 455
14GLNGLNVALVAL(chain A and (resid 264 through 268 or (resid 269...AA264 - 70910 - 455
15GLNGLNVALVAL(chain A and (resid 264 through 268 or (resid 269...AA264 - 70910 - 455
16GLNGLNVALVAL(chain A and (resid 264 through 268 or (resid 269...AA264 - 70910 - 455
21GLNGLNSERSER(chain B and (resid 264 through 268 or (resid 269...BB264 - 26810 - 14
22GLNGLNGLNGLN(chain B and (resid 264 through 268 or (resid 269...BB26915
31GLNGLNPHEPHE(chain C and (resid 264 through 521 or (resid 522...CC264 - 52110 - 267
32ARGARGARGARG(chain C and (resid 264 through 521 or (resid 522...CC522268

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Components

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


Mass: 52521.613 Da / Num. of mol.: 3 / Mutation: R676L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgef16 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH7.5, 0.8 M NAH2PO4, 0.8 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 51159 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Χ2: 0.575 / Net I/σ(I): 3.2 / Num. measured all: 339343
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.056.71.01525280.6540.4211.1010.423100
3.05-3.116.70.85525410.7240.3540.9260.429100
3.11-3.176.70.73425110.7760.3050.7960.437100
3.17-3.236.70.62925380.8130.2610.6820.42499.9
3.23-3.36.70.5325110.8610.2190.5740.447100
3.3-3.386.70.4325400.9080.1790.4660.452100
3.38-3.466.70.34525480.9320.1430.3740.464100
3.46-3.566.50.27125220.9570.1150.2950.48799.9
3.56-3.665.90.22925480.9580.1030.2510.51299.9
3.66-3.786.40.19525350.9740.0830.2120.563100
3.78-3.917.10.16525380.9840.0660.1780.605100
3.91-4.0770.15225790.9850.0610.1640.647100
4.07-4.2670.13725250.9870.0560.1480.697100
4.26-4.486.90.12725530.9880.0520.1370.843100
4.48-4.766.80.11525640.9910.0470.1240.873100
4.76-5.136.50.09725740.9930.0410.1060.718100
5.13-5.645.90.09225750.9920.0410.1010.539100
5.64-6.4670.09326020.9940.0380.1010.50399.9
6.46-8.136.80.07526100.9950.0310.0810.60299.9
8.13-5060.05827170.9960.0250.0630.80299.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CSO

7cso


Resolution: 3→36.77 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 2592 5.08 %RANDOM
Rwork0.212 48419 --
obs0.2142 51011 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.03 Å2 / Biso mean: 69.6351 Å2 / Biso min: 20.59 Å2
Refinement stepCycle: final / Resolution: 3→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10175 0 0 0 10175
Num. residues----1275
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3765X-RAY DIFFRACTION6.734TORSIONAL
12B3765X-RAY DIFFRACTION6.734TORSIONAL
13C3765X-RAY DIFFRACTION6.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.060.32831150.3262283239890
3.06-3.110.3841590.293225302689100
3.11-3.180.35851430.278725292672100
3.18-3.250.30031240.269325652689100
3.25-3.320.30551350.256825282663100
3.32-3.40.3281340.255825672701100
3.4-3.50.28731400.234725122652100
3.5-3.60.24211310.221825362667100
3.6-3.720.27041410.212125692710100
3.72-3.850.25271550.205325232678100
3.85-40.23981170.196225772694100
4-4.180.23751300.189125602690100
4.18-4.40.23261390.180525472686100
4.4-4.680.23561280.174926032731100
4.68-5.040.22091420.174825532695100
5.04-5.550.24071460.204425622708100
5.55-6.340.27081320.233426102742100
6.35-7.980.22451460.22382606275299
7.98-36.770.22551350.19382659279497

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