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- PDB-4xpm: Crystal structure of EGO-TC -

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Basic information

Entry
Database: PDB / ID: 4xpm
TitleCrystal structure of EGO-TC
Components
  • Protein MEH1
  • Protein SLM4
  • Uncharacterized protein YCR075W-A
KeywordsPROTEIN BINDING / EGO complex / Ego1 / Ego2 / Ego3 / TOR signaling / rapamycin
Function / homology
Function and homology information


Ragulator complex / microautophagy / protein localization to vacuole / TORC1 signaling / vacuolar acidification / endocytic recycling / fungal-type vacuole membrane / lysosome organization / positive regulation of TOR signaling / regulation of receptor recycling ...Ragulator complex / microautophagy / protein localization to vacuole / TORC1 signaling / vacuolar acidification / endocytic recycling / fungal-type vacuole membrane / lysosome organization / positive regulation of TOR signaling / regulation of receptor recycling / cholesterol homeostasis / cellular response to amino acid stimulus / protein transport / late endosome / late endosome membrane / positive regulation of MAPK cascade / membrane raft / signal transduction / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Profilin-like / YNR034W-A-like / YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator ...Profilin-like / YNR034W-A-like / YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SLM4 / Protein MEH1 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPowis, K. / Zhang, T. / De Virgilio, C. / Ding, J.
CitationJournal: Cell Res. / Year: 2015
Title: Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling.
Authors: Powis, K. / Zhang, T. / Panchaud, N. / Wang, R. / De Virgilio, C. / Ding, J.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein MEH1
B: Uncharacterized protein YCR075W-A
C: Protein SLM4


Theoretical massNumber of molelcules
Total (without water)30,8913
Polymers30,8913
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-33 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.118, 48.118, 223.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide Protein MEH1 / EGO complex subunit 1 / GSE complex subunit 2


Mass: 4326.944 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 146-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MEH1, EGO1, GSE2, YKR007W, YK106 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q02205
#2: Protein Uncharacterized protein YCR075W-A


Mass: 8192.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YCR075W-A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q3E830
#3: Protein Protein SLM4 / EGO complex subunit 3 / GSE complex subunit 1


Mass: 18371.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SLM4, EGO3, GSE1, YBR077C, YBR0723 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P38247
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M NaCl, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11033 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FTX, 3MS6

4ftx

3ms6


Resolution: 2.4→40.414 Å / FOM work R set: 0.8591 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 528 4.79 %Random
Rwork0.1707 10503 --
obs0.1728 11031 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.66 Å2 / Biso mean: 50.01 Å2 / Biso min: 15.62 Å2
Refinement stepCycle: final / Resolution: 2.4→40.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 58 1997
Biso mean---47.17 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081969
X-RAY DIFFRACTIONf_angle_d1.0872658
X-RAY DIFFRACTIONf_chiral_restr0.073314
X-RAY DIFFRACTIONf_plane_restr0.004334
X-RAY DIFFRACTIONf_dihedral_angle_d15.168724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4013-2.64290.27011360.197425392675100
2.6429-3.02520.22621510.187725362687100
3.0252-3.8110.21911270.157826272754100
3.811-40.41930.19041140.16472801291599
Refinement TLS params.

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

IDL11 (°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)
13.91770.07611.67230.60320.41590.9583-0.58211.4634-1.0767-0.9879-0.0375-0.32550.2629-0.87230.51540.4491-0.11850.21831.1215-0.20980.736-11.5871-11.1702-40.6631
24.94110.06120.38011.33050.10461.2474-0.07030.0209-0.29040.0460.0011-0.04310.03780.1792-0.14180.0535-0.00370.00890.7007-0.18310.3399-10.6328-10.0025-24.0843
35.6294-0.743-0.25460.88580.37642.8291-0.6781-0.4114-0.94760.62680.394-0.04941.9951.66310.23540.67830.2316-0.00180.4926-0.140.5127-14.0984-6.42395.1507
43.50030.3716-0.68654.70790.42444.3653-0.26510.1694-0.0001-0.49190.0531-0.0535-0.83370.10940.16130.2654-0.0765-0.05070.4819-0.08530.3008-20.26380.579-29.5381
59.76945.39550.42065.0261-4.19319.59350.19080.4051-0.7105-0.0918-0.5612-0.42390.49510.51860.23780.1715-0.0178-0.00640.4097-0.17830.4345-23.3093-15.2834-34.5123
62.68462.9356-0.37327.0252-1.39577.8974-0.67271.05360.4058-0.6114-0.1687-0.2323-0.86530.6770.58290.3043-0.149-0.13390.60720.02540.3285-19.6816-4.8424-40.6743
76.7467-0.72070.3984.17390.71814.499-0.18910.4582-0.1354-0.27080.030.0188-0.21390.69140.25630.168-0.0976-0.01830.5553-0.06620.2363-17.4281-6.8879-32.4757
81.90540.1851-0.61912.4141.02887.9524-0.3072-0.19470.3180.15180.2111-0.019-0.36050.79850.01240.31090.006-0.04940.3721-0.13130.3203-15.96132.6958-4.1143
96.9991-2.23471.89980.9903-1.38574.5471-0.3059-0.0330.40670.1131-0.02550.4555-1.089-0.95660.30160.53970.2580.02820.6204-0.12750.4992-29.30378.4646-3.1498
106.74661.5652-1.01363.6698-1.29858.6051-0.1528-0.04270.03860.53790.23390.9535-0.3397-0.9407-0.03630.22660.05920.07540.3867-0.11580.3393-28.5171-1.9885-7.7953
115.07630.5632-1.66475.2844-3.19559.168-0.2628-0.104-0.14350.36740.02010.12550.21060.09710.21180.19840.030.00440.2311-0.08130.208-21.9671-1.7255-5.6321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 146 through 153 )A0
2X-RAY DIFFRACTION2chain A and (resid 154 through 171 )A0
3X-RAY DIFFRACTION3chain A and (resid 172 through 184 )A0
4X-RAY DIFFRACTION4chain B and (resid 8 through 40 )B0
5X-RAY DIFFRACTION5chain B and (resid 41 through 47 )B0
6X-RAY DIFFRACTION6chain B and (resid 48 through 55 )B0
7X-RAY DIFFRACTION7chain B and (resid 56 through 74 )B0
8X-RAY DIFFRACTION8chain C and (resid 2 through 44 )C0
9X-RAY DIFFRACTION9chain C and (resid 45 through 94 )C0
10X-RAY DIFFRACTION10chain C and (resid 95 through 126 )C0
11X-RAY DIFFRACTION11chain C and (resid 127 through 161 )C0

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