PDB-3ulb: Crystal structure of the pleckstrin homology domain of Saccharomy...

ID or keywords:

Entry

Database: PDB / ID: 3ulb

Title

Crystal structure of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a TORC2 subunit, in the P212121 crystal form

Components

Target of rapamycin complex 2 subunit AVO1

Keywords

MEMBRANE PROTEIN / PH domain / membrane localization

Function / homology

Function and homology information

PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / Regulation of TP53 Degradation / TORC2 signaling / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Pan, D. / Matsuura, Y.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2
Authors: Pan, D. / Matsuura, Y.

History

Deposition	Nov 10, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2013	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Nov 1, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ulb.cif.gz	101.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3ulb.ent.gz	79.2 KB	Display	PDB format
PDBx/mmJSON format	3ulb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3ulb_validation.pdf.gz	434.9 KB	Display	wwPDB validaton report
Full document	3ulb_full_validation.pdf.gz	438.6 KB	Display
Data in XML	3ulb_validation.xml.gz	11.2 KB	Display
Data in CIF	3ulb_validation.cif.gz	15.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulb ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulb	HTTPS FTP

-
Related structure data

Related structure data	3ulcC 3voqC 2codS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1c7e-d 2oy2-d 1c7f-d 1qag-1 1xiz-d 1fbz-d 1ab5-d 2vxp-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#108 - Dec 2008 Hsp90 similarity (1) #161 - May 2013 Ricin similarity (1)

Deposited unit

A: Target of rapamycin complex 2 subunit AVO1

B: Target of rapamycin complex 2 subunit AVO1

29.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	40.775, 75.701, 92.231
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Target of rapamycin complex 2 subunit AVO1 / TORC2 subunit AVO1 / Adheres voraciously to TOR2 protein 1 Mass: 14608.734 Da / Num. of mol.: 2 / Fragment: PH domain, residues 1056-1176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: AVO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08236
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Target of rapamycin complex 2 subunit AVO1 / TORC2 subunit AVO1 / Adheres voraciously to TOR2 protein 1

Mass: 14608.734 Da / Num. of mol.: 2 / Fragment: PH domain, residues 1056-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: AVO1 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q08236

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: 0.1M Tris-HCl, 32% MPD, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2009
Radiation	Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→37.85 Å / Num. all: 23155 / Num. obs: 22483 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.051
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.611 / Mean I/σ(I) obs: 2.7 / % possible all: 92.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.1	data extraction
SERGUI		data collection
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2COD

2cod

Resolution: 1.9→37.29 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.901 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2703	1123	5 %	RANDOM
R_work	0.214	-	-	-
all	0.2166	23155	-	-
obs	0.2166	22445	96.69 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 112.76 Å² / B_iso mean: 45.5361 Å² / B_iso min: 19.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→37.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1644	0	0	116	1760

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	1677
X-RAY DIFFRACTION	r_angle_refined_deg	1.937	1.938	2259
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.526	5	195
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.613	22.771	83
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.621	15	306
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.439	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.152	0.2	249
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1249

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.348	73	-
R_work	0.313	1346	-
all	-	1419	-
obs	-	-	89.13 %

Refinement TLS params.

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

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	10.2072	9.6552	-9.2858	9.1396	-8.7715	8.4738	0.2606	0.8458	1.3995	0.1329	0.9675	1.3107	-0.1966	-0.6364	-1.2281	0.1788	-0.252	0.1371	0.8408	-0.0448	0.4309	33.132	37.986	-17.825
2	5.1278	2.8928	0.9858	7.5835	-1.7984	5.5163	0.2264	-0.5865	0.3774	0.2542	-0.3698	0.3162	-0.1192	-0.3376	0.1434	0.1037	-0.005	0.0741	0.1053	-0.0145	0.0994	26.758	34.861	-3.406
3	6.248	-2.8915	-17.1654	2.6917	7.2308	49.0936	-0.0677	0.152	0.0277	-0.3014	-0.381	0.0117	-0.1416	0.0361	0.4487	0.3283	-0.1024	-0.023	0.3909	0.0439	0.3109	21.408	32.492	15.591
4	7.5743	3.0712	-5.1736	7.4062	-1.0255	4.6264	0.1248	-0.1806	0.1918	0.0544	0.055	0.2481	-0.0759	0.0316	-0.1798	0.0759	0.0048	0.0573	0.0751	-0.0546	0.15	4.898	32.806	32.977
5	12.122	8.4957	-6.3142	40.9303	-18.5292	8.9836	-0.2043	1.2161	1.0939	-2.1786	0.6949	0.2056	0.9235	-0.612	-0.4906	0.4009	0.0435	0.0978	0.1609	0.1186	0.4341	3.368	37.947	24.985
6	8.9816	1.6515	-3.3471	4.4859	-1.5741	3.0129	0.1895	-0.4079	-0.7297	0.1685	-0.3305	-0.1287	0.1532	0.3229	0.141	0.1243	-0.0107	0.0002	0.0706	-0.0121	0.1216	11.576	22.36	30.929
7	18.8043	-3.4962	10.9924	12.4938	10.5148	19.7439	0.1913	0.8359	0.0842	-0.6709	-0.9191	0.6144	-0.5768	-0.3076	0.7279	0.2219	-0.1047	0.0772	0.2913	0.0226	0.3983	-2.106	19.959	21.974
8	24.6491	0.6787	4.2795	0.6808	4.5322	30.2626	-0.3617	2.6213	0.1695	-0.4585	-0.0668	0.0496	-2.8918	-0.7708	0.4285	0.8068	0.0237	-0.0402	0.3655	-0.0545	0.1133	6.679	22.054	21.525
9	3.5676	-0.7798	-1.2194	4.2209	-0.893	2.2853	0.1993	-0.8424	-0.3459	0.5959	0.0016	-0.1145	-0.1188	0.4442	-0.2009	0.2074	-0.1001	-0.0513	0.2765	0.0453	0.1448	13.316	26.071	36.874
10	11.4023	17.7215	-0.8994	27.569	-1.701	7.4255	0.463	0.6248	-0.2914	0.4133	1.2533	-0.3364	0.7303	-0.4196	-1.7163	0.5037	0.0388	0.0356	0.4473	0.2368	0.6905	0.132	14.401	39.564
11	6.1189	-1.3876	1.7928	4.4399	0.272	6.5867	0.0529	-0.2052	0.8271	0.2617	-0.067	-0.1207	-0.1524	-0.3681	0.0142	0.1135	-0.0398	0.0591	0.0965	-0.0781	0.1727	13.22	34.083	31.201
12	5.3971	7.879	-15.1965	11.5881	-21.3065	51.9364	-0.1322	0.6518	-0.0152	-0.0499	0.9754	-0.0891	0.0578	-0.4894	-0.8432	0.247	-0.0495	0.1742	0.6584	-0.0538	0.206	17.595	31.659	13.558
13	14.0965	10.4813	-7.4617	13.407	-6.0348	4.0074	0.1131	-0.5512	0.8083	0.7563	0.1318	0.3947	-0.0303	0.1965	-0.2449	0.2612	0.0269	0.1245	0.3754	-0.1675	0.2274	25.24	36.886	0.718
14	8.1927	-1.9518	-2.4107	8.2876	1.272	2.1038	0.1755	-0.2849	0.2147	0.374	0.0808	-0.1916	0.0287	0.1976	-0.2562	0.1015	-0.0005	0.0119	0.0491	0.0139	0.0938	37.753	34.315	-10.1
15	6.4501	0.0829	-2.0111	4.4161	-2.5376	2.5823	0.2539	-0.1984	-0.0462	0.4687	-0.1031	-0.2707	-0.1973	0.2093	-0.1509	0.1607	0.0168	-0.0967	0.0505	-0.0385	0.2064	38.796	25.191	-8.541
16	14.1634	-2.1316	1.0072	4.8251	0.4485	1.7021	0.2224	-0.1629	-0.4792	0.3273	-0.1792	0.3324	0.1189	-0.1312	-0.0432	0.0962	-0.0172	0.0023	0.0433	0.0054	0.0688	25.787	24.128	-7.316
17	10.3908	-11.5391	-1.4333	12.9853	0.7277	4.5628	-0.3328	-0.1864	-0.1033	0.3796	0.2121	0.0955	-0.0146	0.0065	0.1207	0.2023	0.0356	-0.0726	0.1061	0.0632	0.0874	39.434	18.386	-0.093
18	4.2696	-3.1668	2.1917	11.973	-2.4978	3.3295	0.0766	-0.2251	0.256	0.497	0.1201	0.1484	-0.1392	0.0566	-0.1967	0.1091	-0.006	0.048	0.0633	-0.0072	0.095	26.683	30.392	-5.199
19	15.925	-8.142	-2.5773	6.7042	2.482	1.5897	0.415	0.8563	0.1716	-0.2251	-0.2488	-0.0621	-0.233	-0.1591	-0.1663	0.1216	0.0507	-0.0005	0.0931	0.025	0.069	28.16	27.493	-16.861
20	5.2021	0.3927	4.5431	24.4656	13.2091	10.7707	0.1581	0.1062	0.0301	-0.1143	0.6043	-1.397	0.1616	0.3749	-0.7624	0.2529	-0.0105	-0.0362	0.2086	-0.0914	0.2317	39.785	16.811	-18.811

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1066 - 1069
2	X-RAY DIFFRACTION	2	A	1070 - 1075
3	X-RAY DIFFRACTION	3	A	1076 - 1082
4	X-RAY DIFFRACTION	4	A	1083 - 1098
5	X-RAY DIFFRACTION	5	A	1099 - 1113
6	X-RAY DIFFRACTION	6	A	1114 - 1136
7	X-RAY DIFFRACTION	7	A	1137 - 1142
8	X-RAY DIFFRACTION	8	A	1143 - 1147
9	X-RAY DIFFRACTION	9	A	1148 - 1168
10	X-RAY DIFFRACTION	10	A	1169 - 1174
11	X-RAY DIFFRACTION	11	B	1068 - 1074
12	X-RAY DIFFRACTION	12	B	1075 - 1079
13	X-RAY DIFFRACTION	13	B	1080 - 1084
14	X-RAY DIFFRACTION	14	B	1085 - 1110
15	X-RAY DIFFRACTION	15	B	1111 - 1122
16	X-RAY DIFFRACTION	16	B	1123 - 1138
17	X-RAY DIFFRACTION	17	B	1139 - 1146
18	X-RAY DIFFRACTION	18	B	1147 - 1152
19	X-RAY DIFFRACTION	19	B	1153 - 1168
20	X-RAY DIFFRACTION	20	B	1169 - 1174

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi