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- PDB-6fne: Structure of human Brag2 (Sec7-PH domains) with the inhibitor Bra... -

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Basic information

Entry
Database: PDB / ID: 6fne
TitleStructure of human Brag2 (Sec7-PH domains) with the inhibitor Bragsin bound to the PH domain
ComponentsIQ motif and SEC7 domain-containing protein 1
KeywordsHYDROLASE / ARF GEF
Function / homology
Function and homology information


dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding ...dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding / nucleolus / membrane
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 / IQ motif profile. / Pleckstrin homology domain. ...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 / IQ motif profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Chem-DY5 / IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsNawrotek, A. / Zeghouf, M. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
INCA France
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling.
Authors: Nawrotek, A. / Benabdi, S. / Niyomchon, S. / Kryszke, M.H. / Ginestier, C. / Caneque, T. / Tepshi, L. / Mariani, A. / St Onge, R.P. / Giaever, G. / Nislow, C. / Charafe-Jauffret, E. / ...Authors: Nawrotek, A. / Benabdi, S. / Niyomchon, S. / Kryszke, M.H. / Ginestier, C. / Caneque, T. / Tepshi, L. / Mariani, A. / St Onge, R.P. / Giaever, G. / Nislow, C. / Charafe-Jauffret, E. / Rodriguez, R. / Zeghouf, M. / Cherfils, J.
History
DepositionFeb 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 25, 2020Group: Refinement description / Structure summary / Category: software / struct / Item: _software.name / _struct.title
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,4754
Polymers94,7852
Non-polymers6902
Water32418
1
A: IQ motif and SEC7 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0823
Polymers47,3931
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)47,3931
Polymers47,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.912, 66.161, 218.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IQ motif and SEC7 domain-containing protein 1 / ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine ...ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine nucleotide-exchange protein 2 / Brefeldin-resistant Arf-GEF 2 protein / BRAG2


Mass: 47392.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1, ARFGEP100, BRAG2, KIAA0763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#2: Chemical ChemComp-DY5 / (2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one


Mass: 275.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8F3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 18% PEG 20000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→65.9 Å / Num. all: 286171 / Num. obs: 21954 / % possible obs: 93.9 % / Redundancy: 13 % / Biso Wilson estimate: 70.64 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.18 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.78 Å / Num. measured obs: 11487 / Num. unique all: 1099 / Num. unique obs: 11487 / Rpim(I) all: 0.46 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPROCdata collection
STARANISOdata scaling
Cootmodel building
BUSTERrefinement
PHENIXmodel building
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NLY

5nly


Resolution: 2.501→63.33 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 1093 4.98 %RANDOM
Rwork0.2176 ---
obs0.2209 21952 64.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→63.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 47 18 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095788
X-RAY DIFFRACTIONf_angle_d1.1367769
X-RAY DIFFRACTIONf_dihedral_angle_d22.7063583
X-RAY DIFFRACTIONf_chiral_restr0.055841
X-RAY DIFFRACTIONf_plane_restr0.0061013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5015-2.61530.3747150.3022209X-RAY DIFFRACTION5
2.6153-2.75320.3332360.3283661X-RAY DIFFRACTION17
2.7532-2.92570.2966660.29211213X-RAY DIFFRACTION31
2.9257-3.15160.3441150.29682448X-RAY DIFFRACTION61
3.1516-3.46880.36142020.26453981X-RAY DIFFRACTION99
3.4688-3.97060.29121940.22764019X-RAY DIFFRACTION100
3.9706-5.00230.24592070.18154083X-RAY DIFFRACTION100
5.0023-63.34990.25762580.19994245X-RAY DIFFRACTION100

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