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- PDB-4wpc: Crystal structure of Rgd1p F-BAR domain in complex with inositol ... -

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Basic information

Entry
Database: PDB / ID: 4wpc
TitleCrystal structure of Rgd1p F-BAR domain in complex with inositol phosphate
ComponentsRHO GTPase-activating protein RGD1
KeywordsLIPID BINDING PROTEIN / F-BAR domain / phospholipid binding / PROTEIN BINDING
Function / homology
Function and homology information


RHOF GTPase cycle / CDC42 GTPase cycle / septin ring organization / RHOD GTPase cycle / RHOV GTPase cycle / site of polarized growth / cellular bud / prospore membrane / phosphatidylinositol-5-phosphate binding / actin cortical patch ...RHOF GTPase cycle / CDC42 GTPase cycle / septin ring organization / RHOD GTPase cycle / RHOV GTPase cycle / site of polarized growth / cellular bud / prospore membrane / phosphatidylinositol-5-phosphate binding / actin cortical patch / cell tip / response to acidic pH / phosphatidylinositol-3-phosphate binding / mating projection tip / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to osmotic stress / small GTPase-mediated signal transduction / cell division site / establishment of cell polarity / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / actin cytoskeleton organization / cell cortex / identical protein binding / plasma membrane
Similarity search - Function
: / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain ...: / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Rho GTPase activation protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RHO GTPase-activating protein RGD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsMoravcevic, K. / Lemmon, M.A.
CitationJournal: Structure / Year: 2015
Title: Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site.
Authors: Moravcevic, K. / Alvarado, D. / Schmitz, K.R. / Kenniston, J.A. / Mendrola, J.M. / Ferguson, K.M. / Lemmon, M.A.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Sep 23, 2015Group: Non-polymer description
Revision 1.4Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHO GTPase-activating protein RGD1
B: RHO GTPase-activating protein RGD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0794
Polymers73,7592
Non-polymers1,3202
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-80 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.993, 74.110, 105.734
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RHO GTPase-activating protein RGD1 / RhoGAP / Related GAP domain protein 1


Mass: 36879.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RGD1, YBR260C, YBR1728 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P38339
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.61 Å3/Da / Density % sol: 73.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate, pH 5.5, containing 0.1-0.2 M (NH4)2SO4 plus 10-20% (w/v) PEG3350
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 19341 / % possible obs: 99.7 % / Redundancy: 4.2 % / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4WPE

4wpe


Resolution: 3.34→30.773 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3 993 5.15 %
Rwork0.2613 --
obs0.2632 19300 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→30.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 72 8 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014444
X-RAY DIFFRACTIONf_angle_d1.1156046
X-RAY DIFFRACTIONf_dihedral_angle_d16.1751556
X-RAY DIFFRACTIONf_chiral_restr0.459733
X-RAY DIFFRACTIONf_plane_restr0.002746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3402-3.51610.34761430.33452341X-RAY DIFFRACTION89
3.5161-3.7360.40211390.31562654X-RAY DIFFRACTION100
3.736-4.02390.31671480.29382627X-RAY DIFFRACTION99
4.0239-4.42780.27511540.25912634X-RAY DIFFRACTION99
4.4278-5.06610.25471460.22232643X-RAY DIFFRACTION100
5.0661-6.37340.3131210.26992708X-RAY DIFFRACTION100
6.3734-30.77480.26011420.22082700X-RAY DIFFRACTION98

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