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- PDB-6fae: The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPas... -

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Basic information

Entry
Database: PDB / ID: 6fae
TitleThe Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1
Components
  • ADP-ribosylation factor 1ARF1
  • IQ motif and SEC7 domain-containing protein 2
KeywordsHYDROLASE / GTPase GEF
Function / homology
Function and homology information


Glycosphingolipid transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / regulation of ARF protein signal transduction / Nef Mediated CD4 Down-regulation / dendritic spine organization ...Glycosphingolipid transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / regulation of ARF protein signal transduction / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / guanyl-nucleotide exchange factor activity / small monomeric GTPase / intracellular protein transport / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cellular response to virus / actin cytoskeleton organization / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-ribosylation factor 1 / IQ motif and SEC7 domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsGray, J. / Krojer, T. / Fairhead, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Nuffield Department of Medicine, University of Oxford United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Targeting the Small GTPase Superfamily through their Regulatory Proteins.
Authors: Gray, J.L. / von Delft, F. / Brennan, P.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IQ motif and SEC7 domain-containing protein 2
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4483
Polymers67,3862
Non-polymers621
Water2,468137
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-5 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.995, 92.744, 66.895
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IQ motif and SEC7 domain-containing protein 2


Mass: 43601.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC2, KIAA0522 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JU85
#2: Protein ADP-ribosylation factor 1 / ARF1


Mass: 23784.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84077
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M tris 16% PEG 8K 0.1M Potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.35→49.14 Å / Num. obs: 25045 / % possible obs: 99.9 % / Redundancy: 3.3 % / Net I/σ(I): 8.9
Reflection shellResolution: 2.35→2.41 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementResolution: 2.35→49.134 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.91
RfactorNum. reflection% reflection
Rfree0.2851 1161 4.73 %
Rwork0.2405 --
obs0.2426 24553 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 4 137 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013949
X-RAY DIFFRACTIONf_angle_d0.3925342
X-RAY DIFFRACTIONf_dihedral_angle_d14.6572374
X-RAY DIFFRACTIONf_chiral_restr0.039604
X-RAY DIFFRACTIONf_plane_restr0.002696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3499-2.45680.43341530.38262805X-RAY DIFFRACTION95
2.4568-2.58630.39131410.33532915X-RAY DIFFRACTION98
2.5863-2.74830.38471390.29822879X-RAY DIFFRACTION98
2.7483-2.96050.32311490.28142931X-RAY DIFFRACTION99
2.9605-3.25840.31451520.2622971X-RAY DIFFRACTION99
3.2584-3.72980.27641390.24732912X-RAY DIFFRACTION97
3.7298-4.69850.25111350.18562968X-RAY DIFFRACTION99
4.6985-49.14450.21181530.19363011X-RAY DIFFRACTION99

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