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- PDB-2v6v: The structure of the Bem1p PX domain -

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Basic information

Entry
Database: PDB / ID: 2v6v
TitleThe structure of the Bem1p PX domain
ComponentsBUD EMERGENCE PROTEIN 1
KeywordsREGULATOR / HOMOTYPIC FUSION / PI3P / 3-KINASE / PX DOMAIN / SH3 DOMAIN / CYTOSKELETON / CELL POLARITY / PHOSPHORYLATION / PHOSPHOINOSITIDE
Function / homology
Function and homology information


positive regulation of vacuole fusion, non-autophagic / RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / site of polarized growth / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location ...positive regulation of vacuole fusion, non-autophagic / RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / site of polarized growth / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location / cellular bud neck / regulation of Rho protein signal transduction / mating projection tip / phosphatidylinositol-3-phosphate binding / cell cortex / protein-macromolecule adaptor activity / molecular adaptor activity / cytoskeleton / mitochondrion / cytoplasm
Similarity search - Function
Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / Phox-like domain / PX Domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / Phox-like domain / PX Domain / PB1 domain / PB1 domain / : / PB1 domain profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Bud emergence protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsStahelin, R.V. / Karathanassis, D. / Murray, D. / Williams, R.L. / Cho, W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Membrane Binding Analysis of the Phox Homology Domain of Bem1P: Basis of Phosphatidylinositol 4-Phosphate Specificity.
Authors: Stahelin, R.V. / Karathanassis, D. / Murray, D. / Williams, R.L. / Cho, W.
History
DepositionJul 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BUD EMERGENCE PROTEIN 1
B: BUD EMERGENCE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4813
Polymers36,3262
Non-polymers1541
Water7,909439
1
A: BUD EMERGENCE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3172
Polymers18,1631
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BUD EMERGENCE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)18,1631
Polymers18,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.015, 71.621, 75.316
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 BUD EMERGENCE PROTEIN 1 / BEM1P / SUPPRESSOR OF RHO3 PROTEIN 1


Mass: 18163.189 Da / Num. of mol.: 2 / Fragment: PX DOMAIN, RESIDUES 266-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PJL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 834(DE3) / References: UniProt: P29366
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNECESSARY FOR CELL POLARIZATION DURING VEGETATIVE GROWTH
Has protein modificationY
Sequence detailsRESIDUES 266-413 PLUS GSHHHHHH FROM THE PJL VECTOR

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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: 2.5 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6.2
Details: 0.2 M NACL, 0.1 M NA/K PHOSPHATE PH 6.2, 10% PEG 8000 AND 2 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.5→51.9 Å / Num. obs: 164846 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.89
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.5→51.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.644 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2706 5.1 %RANDOM
Rwork0.222 ---
obs0.224 50498 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 8 439 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9723017
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9225267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58624.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.661514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21054
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21576
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.51375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48522165
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3293976
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.154.5852
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 199
Rwork0.35 3677

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