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- PDB-4jmo: Complexe of ARNO Sec7 domain with the protein-protein interaction... -

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Basic information

Entry
Database: PDB / ID: 4jmo
TitleComplexe of ARNO Sec7 domain with the protein-protein interaction inhibitor N-(4-hydroxy-2,6-dimethylphenyl)-4-methoxybenzenesulfonamide
ComponentsCytohesin-2CYTH2
KeywordsSIGNALING PROTEIN/INHIBITOR / Nucleotide exchange factor / ARF1 / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of ARF protein signal transduction / Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane ...regulation of ARF protein signal transduction / Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane / lipid binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 ...Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JAF / Cytohesin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoh, F. / Rouhana, J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors
Authors: Rouhana, J. / Hoh, F. / Estaran, S. / Henriquet, C. / Boublik, Y. / Kerkour, A. / Trouillard, R. / Martinez, J. / Pugniere, M. / Padilla, A. / Chavanieu, A.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Structure summary
Revision 1.3Apr 23, 2014Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytohesin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3372
Polymers23,0291
Non-polymers3071
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.940, 89.940, 89.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Cytohesin-2 / CYTH2 / ARF exchange factor / ARF nucleotide-binding site opener / Protein ARNO / PH / SEC7 and coiled-coil ...ARF exchange factor / ARF nucleotide-binding site opener / Protein ARNO / PH / SEC7 and coiled-coil domain-containing protein 2


Mass: 23029.312 Da / Num. of mol.: 1 / Fragment: Sec7 domain, UNP residues 56-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYTH2, ARNO, PSCD2, PSCD2L / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99418
#2: Chemical ChemComp-JAF / N-(4-hydroxy-2,6-dimethylphenyl)-4-methoxybenzenesulfonamide


Mass: 307.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MgSO4,Peg5K MME 18%, 0.1M Tris-HCl, pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→40.22 Å / Num. obs: 22395 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.321 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JMI

4jmi


Resolution: 1.8→40.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.335 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 3.5 / ESU R: 0.162 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21021 1148 5.1 %RANDOM
Rwork0.1516 ---
obs0.15471 22395 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.883 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 21 179 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191631
X-RAY DIFFRACTIONr_bond_other_d0.0010.021577
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9842202
X-RAY DIFFRACTIONr_angle_other_deg0.8363.0043613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6424.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1621514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_rigid_bond_restr4.01733208
X-RAY DIFFRACTIONr_sphericity_free29.392549
X-RAY DIFFRACTIONr_sphericity_bonded13.85153303
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 82 -
Rwork0.211 1579 -
obs--99.46 %

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