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- PDB-3o5z: Crystal structure of the SH3 domain from p85beta subunit of phosp... -

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Basic information

Entry
Database: PDB / ID: 3o5z
TitleCrystal structure of the SH3 domain from p85beta subunit of phosphoinositide 3-kinase (PI3K)
ComponentsPhosphatidylinositol 3-kinase regulatory subunit beta
KeywordsPROTEIN BINDING / Src homology 3 domain
Function / homology
Function and homology information


IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / RHOF GTPase cycle / RHOD GTPase cycle / regulation of stress fiber assembly / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle ...IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / RHOF GTPase cycle / RHOD GTPase cycle / regulation of stress fiber assembly / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / RND2 GTPase cycle / PI3K/AKT activation / RND3 GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / RHOB GTPase cycle / Signaling by ALK / negative regulation of MAPK cascade / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / CDC42 GTPase cycle / RHOU GTPase cycle / T cell differentiation / RET signaling / RHOA GTPase cycle / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of cell adhesion / PI3K Cascade / RAC3 GTPase cycle / RAC2 GTPase cycle / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / regulation of protein localization to plasma membrane / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Tie2 Signaling / GPVI-mediated activation cascade / RAC1 GTPase cycle / response to endoplasmic reticulum stress / Interleukin-7 signaling / phosphotyrosine residue binding / Downstream signal transduction / B cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / regulation of autophagy / Regulation of signaling by CBL / Signaling by SCF-KIT / VEGFA-VEGFR2 Pathway / receptor tyrosine kinase binding / positive regulation of protein import into nucleus / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / protein transport / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / insulin receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / G alpha (q) signalling events / protein phosphatase binding / Extra-nuclear estrogen signaling / immune response / protein heterodimerization activity / focal adhesion / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH3 Domains / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsChen, S. / Xiao, Y. / Ponnusamy, R. / Tan, J. / Lei, J. / Hilgenfeld, R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: X-ray structure of the SH3 domain of the phosphoinositide 3-kinase p85 beta subunit
Authors: Chen, S. / Xiao, Y. / Ponnusamy, R. / Tan, J. / Lei, J. / Hilgenfeld, R.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Sep 10, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase regulatory subunit beta
B: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8115
Polymers19,6222
Non-polymers1893
Water41423
1
A: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8472
Polymers9,8111
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9653
Polymers9,8111
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.010, 57.790, 62.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 3-kinase regulatory subunit beta / PtdIns-3-kinase regulatory subunit beta / PI3-kinase regulatory subunit beta / PI3K regulatory ...PtdIns-3-kinase regulatory subunit beta / PI3-kinase regulatory subunit beta / PI3K regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit beta / PtdIns-3-kinase regulatory subunit p85-beta / PI3-kinase subunit p85-beta


Mass: 9811.126 Da / Num. of mol.: 2 / Fragment: SH3 domain, UNP residues 6-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00459
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% MPD, 0.1M sodium cacodylate, 0.05M calcium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 3, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.01→21.4 Å / Num. all: 11654 / Num. obs: 11641 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.3
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1665 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.7 Å
Translation2.5 Å23.7 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→21.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2598 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.789 / SU B: 13.919 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2084 / SU Rfree: 0.1843 / Cross valid method: THROUGHOUT / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 864 7.4 %RANDOM
Rwork0.2119 ---
all0.2119 11654 --
obs0.2156 11641 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.27 Å2 / Biso mean: 53.1861 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 10 23 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221288
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9961747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06322.12166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55515194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7291518
X-RAY DIFFRACTIONr_chiral_restr0.1370.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221034
X-RAY DIFFRACTIONr_mcbond_it1.0271.5792
X-RAY DIFFRACTIONr_mcangle_it1.52221261
X-RAY DIFFRACTIONr_scbond_it2.5573496
X-RAY DIFFRACTIONr_scangle_it3.7624.5486
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 47 -
Rwork0.271 793 -
all-840 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.0456-13.61514.320815.84083.01385.3392-0.3991.0393-0.45431.432-0.26122.71560.7781-1.84660.66020.2818-0.00330.22480.55110.21261.16652.469514.21076.7651
212.00110.4091-5.644811.04831.12446.375-0.01761.1622-0.2161-1.10360.04960.4454-0.254-0.2897-0.0320.1971-0.0054-0.11170.3087-0.03890.109616.98659.7898-1.8585
37.9562-2.49650.544711.289-8.870439.47750.2237-0.2121-1.4523-0.2786-0.1882-1.46181.21231.2048-0.03540.11750.0306-0.08520.3469-0.03190.605525.32483.00584.7644
410.0695-0.228311.717716.81965.5227.11730.7929-0.2803-1.16611.54550.1277-0.97470.0369-0.3428-0.92060.4003-0.0529-0.29930.50920.20070.483524.89224.871913.6495
58.26950.0303-0.90596.90643.888620.58910.37950.1739-1.5376-0.12710.2899-0.65750.6430.5638-0.66940.14020.0205-0.09190.1469-0.07360.353219.96762.78662.2655
65.68091.2796-5.12875.74078.377810.02880.0490.1246-0.4419-0.14770.05070.1446-0.1872-0.3414-0.09970.2484-0.0103-0.07570.30320.00660.577811.6586.54332.8066
79.6903-0.9924-3.582739.85727.20242.78250.1991-0.562-0.1111.7558-0.0631.4572-0.6586-0.9511-0.1360.54120.0480.26430.51280.02360.17667.917916.164113.94
88.5253-7.66026.647811.8298-7.529114.0572-0.1081-0.8631-0.26561.42620.34991.1144-0.0604-0.6359-0.24190.35-0.04520.12790.3313-0.0850.217310.922221.972411.4808
98.5838-0.7984-0.824614.3731-1.013812.21020.11240.19481.25020.31410.0335-0.069-0.3289-0.1093-0.14580.194-0.0024-0.0180.1819-0.04010.157213.977120.4843.5987
101.2298-7.36951.525510.90020.21032.84620.0106-0.08150.20541.09790.1967-0.42370.0892-0.0257-0.20730.4579-0.0386-0.06160.3481-0.01820.16117.981613.06559.8553
110.7333-0.88886.894223.55761.770213.04490.945-0.0738-1.254-0.1904-0.44830.40460.8591-0.3708-0.49680.2152-0.0344-0.21280.18570.00430.641612.20740.4574.2696
127.41122.58085.90136.06851.337211.31490.6216-1.6043-1.480.9894-0.4620.67430.452-0.6749-0.15970.367-0.0631-0.22980.40540.24390.671913.56311.843510.3192
1313.7774-2.37413.136613.977-0.97274.70820.08380.32060.0627-0.32590.0221-0.40590.1054-0.0011-0.10590.1646-0.0129-0.0450.2365-0.0320.072617.716312.7112.0217
1415.73153.89510.762810.65227.7656-2.9482-0.0484-0.0597-1.06250.4773-0.01662.13480.5014-0.10560.06490.1976-0.0146-0.07280.34450.07591.02643.083710.37473.9059
153.7657-1.43281.02634.7567-11.722515.4067-0.1582-0.40681.11152.10420.0440.708-0.48780.40630.11420.9411-0.12980.35820.4074-0.15820.643430.31227.082534.6493
162.38291.12558.48156.2584-7.856815.7766-0.13960.28620.4364-0.5607-0.3269-0.78470.60191.55280.46640.3399-0.11430.04260.58870.04260.548138.975611.332522.5696
1715.26857.75815.199412.3082.78847.1965-0.71660.75750.7912-0.4810.4651-0.4134-1.59930.66020.25140.6115-0.12560.0220.3740.12240.380630.860515.880114.7783
180.0244-11.6247-6.98326.25134.639919.13260.26110.66570.6011-0.3358-0.88840.099-1.5894-0.77590.62730.5835-0.0461-0.18310.35870.18930.660827.346116.563118.9733
1919.1594-3.32422.902518.0463-1.4585-7.5496-0.15570.52570.84430.5724-0.0988-0.1903-0.20570.63680.25450.6104-0.3958-0.11790.54190.05380.344737.549515.496627.5375
204.23572.30150.51767.25242.06715.61950.2605-0.6430.62921.1242-0.33041.4866-0.4462-0.65370.06990.3164-0.00840.11530.2327-0.02190.456923.04545.952331.3189
2113.30882.53182.803221.424-0.0716-1.1671-0.0036-0.0699-0.24250.39510.09581.6668-0.5712-0.1845-0.09210.23760.02220.05840.22350.00920.332122.5999-1.786528.7318
2217.73922.6217-11.440317.1839-3.667521.8060.1561-0.6306-0.52890.4423-0.26350.24210.06690.730.10750.1171-0.042-0.05130.151-0.01450.178531.9038-0.649329.4265
230.86182.32182.326117.384-6.79093.5473-0.18060.17790.3534-0.2430.06151.27720.0685-0.03450.11910.2237-0.0246-0.08930.24960.07380.458427.80154.810722.3104
24-3.0256-8.9803-13.755120.9471-2.945726.31650.5676-1.57070.19882.8516-0.61250.6769-2.53711.51420.04490.8982-0.11770.01890.3237-0.01050.501230.600517.764130.6522
259.0781-1.45861.05418.35110.72797.3874-0.0350.15061.43791.0584-0.0661.6361-1.6844-0.25320.1010.6028-0.04160.06320.09370.09050.639127.266317.229626.6662
266.132-1.24144.542518.8323-3.68219.30350.0170.25270.0947-0.5668-0.0171-0.371-0.11961.40.00020.1253-0.0475-0.05320.2950.01390.122335.9126.650224.033
275.6708-2.7407-6.89745.36364.3122.2243-0.1047-1.54131.08272.1590.05730.8038-0.41710.29390.04740.8271-0.05810.10890.5281-0.09350.375731.3275.802937.6454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 8
2X-RAY DIFFRACTION2A9 - 13
3X-RAY DIFFRACTION3A14 - 17
4X-RAY DIFFRACTION4A18 - 22
5X-RAY DIFFRACTION5A23 - 27
6X-RAY DIFFRACTION6A28 - 33
7X-RAY DIFFRACTION7A34 - 40
8X-RAY DIFFRACTION8A41 - 47
9X-RAY DIFFRACTION9A48 - 53
10X-RAY DIFFRACTION10A54 - 59
11X-RAY DIFFRACTION11A60 - 64
12X-RAY DIFFRACTION12A65 - 69
13X-RAY DIFFRACTION13A70 - 77
14X-RAY DIFFRACTION14A78 - 84
15X-RAY DIFFRACTION15B5 - 10
16X-RAY DIFFRACTION16B11 - 15
17X-RAY DIFFRACTION17B16 - 19
18X-RAY DIFFRACTION18B20 - 24
19X-RAY DIFFRACTION19B25 - 30
20X-RAY DIFFRACTION20B31 - 39
21X-RAY DIFFRACTION21B40 - 47
22X-RAY DIFFRACTION22B48 - 52
23X-RAY DIFFRACTION23B53 - 58
24X-RAY DIFFRACTION24B59 - 63
25X-RAY DIFFRACTION25B64 - 70
26X-RAY DIFFRACTION26B71 - 76
27X-RAY DIFFRACTION27B77 - 82

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