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- PDB-6jwp: crystal structure of EGOC -

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Basic information

Entry
Database: PDB / ID: 6jwp
Titlecrystal structure of EGOC
Components
  • (GTP-binding protein ...) x 2
  • Ego2
  • Protein MEH1
  • Protein SLM4
KeywordsPROTEIN TRANSPORT / EGOC / roadblock domain / Gtr1 / TORC1
Function / homology
Function and homology information


MTOR signalling / Gtr1-Gtr2 GTPase complex / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Amino acids regulate mTORC1 / phosphate ion transport / TORC1 signaling / endocytic recycling ...MTOR signalling / Gtr1-Gtr2 GTPase complex / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Amino acids regulate mTORC1 / phosphate ion transport / TORC1 signaling / endocytic recycling / vacuolar acidification / fungal-type vacuole membrane / cellular response to nitrogen starvation / transcription by RNA polymerase III / regulation of receptor recycling / positive regulation of TOR signaling / subtelomeric heterochromatin formation / transcription by RNA polymerase I / positive regulation of TORC1 signaling / negative regulation of autophagy / cellular response to starvation / cellular response to amino acid stimulus / late endosome membrane / late endosome / protein transport / cellular response to oxidative stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / chromosome, telomeric region / positive regulation of MAPK cascade / membrane raft / GTPase activity / chromatin / GTP binding / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm / cytosol
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 / Beta-Lactamase - #190 / LAMTOR1/MEH1 / 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 / Beta-Lactamase - #190 / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein SLM4 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsZhang, T. / Ding, J.
CitationJournal: Sci Adv / Year: 2019
Title: Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases.
Authors: Zhang, T. / Peli-Gulli, M.P. / Zhang, Z. / Tang, X. / Ye, J. / De Virgilio, C. / Ding, J.
History
DepositionApr 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein GTR1
B: GTP-binding protein GTR2
C: Protein MEH1
D: Ego2
E: Protein SLM4
F: GTP-binding protein GTR1
G: GTP-binding protein GTR2
H: Protein MEH1
I: Ego2
J: Protein SLM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,95616
Polymers232,31610
Non-polymers1,6406
Water00
1
A: GTP-binding protein GTR1
B: GTP-binding protein GTR2
C: Protein MEH1
D: Ego2
E: Protein SLM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2519
Polymers116,1585
Non-polymers1,0934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-128 kcal/mol
Surface area39330 Å2
MethodPISA
2
F: GTP-binding protein GTR1
G: GTP-binding protein GTR2
H: Protein MEH1
I: Ego2
J: Protein SLM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7057
Polymers116,1585
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-112 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.675, 120.547, 323.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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GTP-binding protein ... , 2 types, 4 molecules AFBG

#1: Protein GTP-binding protein GTR1


Mass: 36117.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GTR1 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00582
#2: Protein GTP-binding protein GTR2


Mass: 39092.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GTR2 / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53290

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Protein , 3 types, 6 molecules CHDIEJ

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


Mass: 14471.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02205
#4: Protein Ego2


Mass: 8104.935 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: Gtr2 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3E830
#5: Protein Protein SLM4 / EGO complex subunit 3 / GSE complex subunit 1


Mass: 18371.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: EGO3 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38247

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Non-polymers , 2 types, 6 molecules

#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→49.24 Å / Num. obs: 36895 / % possible obs: 68.9 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.38 Å / Rmerge(I) obs: 1.679 / Num. unique obs: 1853 / CC1/2: 0.461

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R7W

3r7w


Resolution: 3.2→49.24 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.841 / SU B: 70.207 / SU ML: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.645 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2854 1863 5.1 %RANDOM
Rwork0.2301 ---
obs0.2329 35028 68.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 195.98 Å2 / Biso mean: 70.248 Å2 / Biso min: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0 Å2
2---0.44 Å20 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 3.2→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13043 0 99 0 13142
Biso mean--73.08 --
Num. residues----1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01213330
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.62517996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2151635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59724.475619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.15152418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4481542
X-RAY DIFFRACTIONr_chiral_restr0.0860.21837
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029702
X-RAY DIFFRACTIONr_rigid_bond_restr0.291313255
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.565 40 -
Rwork0.41 725 -
all-765 -
obs--19.52 %
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)
10.0734-0.0120.0350.09270.08010.09880.0148-0.0067-0.00540.0318-0.01390.00790.0405-0.0156-0.00090.052-0.0070.00410.02550.00330.009633.658121.26527.708
20.03990.0131-0.02360.0072-0.00860.0144-0.0074-0.0077-0.0085-0.00120.0033-0.00020.00530.00490.00410.0454-0.00070.00310.0327-0.0040.008964.247142.19221.897
30.0709-0.0445-0.00330.04210.0490.1650.00760.00870.0267-0.00360.0031-0.0174-0.00510.029-0.01070.036-0.0007-0.00010.0310.00830.019459.912153.7769.458
40.11480.0663-0.00070.0867-0.11890.2937-0.00870.0012-0.0005-0.00360.00750.0024-0.01510.00120.00120.03620.0001-0.00230.03080.00040.013155.823156.94794.175
50.032-0.02520.03110.0543-0.05920.06560.00670.00840.001-0.0151-0.0030.00380.01270.0046-0.00370.0414-0.00170.00210.0329-0.00020.008948.984143.04570.892
60.00970.02540.01940.0990.1070.1504-0.00620.00040.0075-0.0099-0.00960.0273-0.0111-0.01320.01580.0384-0.00090.00190.0343-0.00390.018618.425118.354-21.91
70.35670.15340.01810.25470.08560.03330.0183-0.0244-0.01280.04780.0013-0.05340.01570.0005-0.01960.04350.0036-0.00630.0340.00120.01947.321105.141-38.702
80.08960.02120.06470.01120.01450.04690.00270.0203-0.0002-0.0104-0.0022-0.00440.00430.0158-0.00050.03560.00410.00050.03170.00090.010432.72884.579-66.066
90.04870.0225-0.09820.03250.00430.3170.01060.0079-0.00780.00550.0101-0.0175-0.00630.0104-0.02070.03280.0149-0.00690.0342-0.01930.016517.37272.773-86.275
100.05490.05380.02070.05960.02420.01140.00040.0063-0.00340.0096-0.00220.00420.00530.00440.00180.0380.0021-0.00010.0356-0.00840.011218.69890.248-64.444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 309
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B10 - 325
4X-RAY DIFFRACTION2B401 - 402
5X-RAY DIFFRACTION3C43 - 184
6X-RAY DIFFRACTION4D8 - 74
7X-RAY DIFFRACTION5E2 - 162
8X-RAY DIFFRACTION6F4 - 309
9X-RAY DIFFRACTION6F401 - 402
10X-RAY DIFFRACTION7G6 - 327
11X-RAY DIFFRACTION8H43 - 184
12X-RAY DIFFRACTION9I10 - 74
13X-RAY DIFFRACTION10J2 - 162

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