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- PDB-6zpn: Crystal structure of Chaetomium thermophilum Raptor -

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Basic information

Entry
Database: PDB / ID: 6zpn
TitleCrystal structure of Chaetomium thermophilum Raptor
ComponentsWD_REPEATS_REGION domain-containing protein
KeywordsPROTEIN BINDING / mTOR Complex 1 / cell growth and metabolism
Function / homology
Function and homology information


TORC1 complex / TOR signaling
Similarity search - Function
Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Raptor N-terminal CASPase-like domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsImseng, S. / Boehm, R. / Jakob, R.P. / Hall, M.N. / Hiller, S. / Maier, T.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation179323 Switzerland
CitationJournal: Mol.Cell / Year: 2021
Title: The dynamic mechanism of 4E-BP1 recognition and phosphorylation by mTORC1.
Authors: Bohm, R. / Imseng, S. / Jakob, R.P. / Hall, M.N. / Maier, T. / Hiller, S.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD_REPEATS_REGION domain-containing protein
B: WD_REPEATS_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)339,2752
Polymers339,2752
Non-polymers00
Water00
1
A: WD_REPEATS_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)169,6381
Polymers169,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD_REPEATS_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)169,6381
Polymers169,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.306, 183.306, 271.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 216 through 416 or resid 432...
21(chain B and (resid 216 through 239 or resid 244...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 216 through 416 or resid 432...A216 - 416
121(chain A and (resid 216 through 416 or resid 432...A432 - 897
131(chain A and (resid 216 through 416 or resid 432...A939 - 991
141(chain A and (resid 216 through 416 or resid 432...A14
151(chain A and (resid 216 through 416 or resid 432...A1467 - 1501
211(chain B and (resid 216 through 239 or resid 244...B216 - 239
221(chain B and (resid 216 through 239 or resid 244...B244 - 266
231(chain B and (resid 216 through 239 or resid 244...B282 - 588
241(chain B and (resid 216 through 239 or resid 244...B128
251(chain B and (resid 216 through 239 or resid 244...B1286 - 1501

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Components

#1: Protein WD_REPEATS_REGION domain-containing protein


Mass: 169637.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0014610 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S1S2

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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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.2-5.3 1.75 M NaCl 12 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 3.5→49.97 Å / Num. obs: 58884 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.989 / Net I/σ(I): 5
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4557 / CC1/2: 0.367 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
DIALSdata scaling
PHASERphasing
DIALSdata processing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EF5

5ef5


Resolution: 3.5→47.61 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.14 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2957 5.04 %Random selection
Rwork0.228 55702 --
obs0.2288 58659 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 367.52 Å2 / Biso mean: 144.9403 Å2 / Biso min: 10.31 Å2
Refinement stepCycle: final / Resolution: 3.5→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17406 0 0 0 17406
Num. residues----2158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6358X-RAY DIFFRACTION13.609TORSIONAL
12B6358X-RAY DIFFRACTION13.609TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.560.40831300.36622628275899
3.56-3.620.33811370.350426152752100
3.62-3.680.45711330.40912582271599
3.68-3.760.3571560.35672597275399
3.76-3.830.30811370.312926332770100
3.83-3.920.37721320.35062557268998
3.92-4.010.37821420.33812586272898
4.01-4.110.24161520.250626162768100
4.11-4.220.22091300.232826392769100
4.22-4.340.27351310.219126452776100
4.34-4.480.24121530.198926312784100
4.48-4.640.21281420.188326422784100
4.64-4.830.16731410.182326662807100
4.83-5.050.22741250.173426522777100
5.05-5.310.19321460.178426592805100
5.31-5.640.23531380.194926762814100
5.64-6.080.22391420.2072664280699
6.08-6.690.22641480.215126802828100
6.69-7.650.25581300.207327412871100
7.65-9.630.17951410.180427522893100
9.63-47.610.2481710.24322841301299
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)
1-0.0437-0.0388-0.37670.01790.15540.13670.37260.24440.12150.36040.00980.3392-0.28830.01480.11881.18840.08620.26090.96910.23481.0736.271886.2589123.9338
22.58260.559-0.28753.14170.25980.58490.3439-0.3359-0.24930.9534-0.18870.1015-0.1460.13120.38531.0723-0.0557-0.03860.68360.02520.676732.69981.2573134.889
31.1872-0.4904-1.31990.16470.52761.29930.16910.51460.138-0.2943-0.0121-0.0348-0.0401-0.193601.1070.01940.07021.0842-0.07791.094851.936193.201886.7465
40.435-0.40680.55190.6341-0.77280.88940.46480.18-0.67020.3104-0.3708-0.40170.11340.21990.0380.99460.06960.1540.8261-0.24371.196377.11384.981784.2276
52.12570.3395-0.07720.1088-0.20010.29190.2378-0.16930.5120.0344-0.0715-0.201-0.28310.32510.42371.3426-0.12510.18071.1642-0.14261.460483.4643120.44891.442
60.8862-0.2642-1.4587-0.3644-0.011.5321-0.08140.053-0.0098-0.02360.10520.02720.2496-0.1048-00.8793-0.19310.04430.90440.03330.927817.048564.0041102.0952
71.75980.4443-0.4141.20071.18851.95050.09250.4465-0.0223-0.3917-0.13780.2699-0.1118-0.24920.00010.85520.0833-0.14720.8606-0.05360.860531.683763.141562.3692
81.6886-0.0071-1.64370.6410.03511.5172-0.3903-0.107-1.11750.54880.06410.00880.264-0.33560.03170.9952-0.0098-0.09080.9273-0.3621.351946.169338.946945.9144
93.02640.4512-0.58520.8831-0.13641.1265-0.184-0.2908-0.07830.01970.1413-0.29030.10910.5347-0.09020.95540.1153-0.11781.1516-0.11.131176.752752.081460.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 216 through 312 )A216 - 312
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 699 )A313 - 699
3X-RAY DIFFRACTION3chain 'A' and (resid 700 through 956 )A700 - 956
4X-RAY DIFFRACTION4chain 'A' and (resid 957 through 1117 )A957 - 1117
5X-RAY DIFFRACTION5chain 'A' and (resid 1118 through 1502 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 212 through 668 )B212 - 668
7X-RAY DIFFRACTION7chain 'B' and (resid 669 through 840 )B669 - 840
8X-RAY DIFFRACTION8chain 'B' and (resid 841 through 1111 )B841 - 1111
9X-RAY DIFFRACTION9chain 'B' and (resid 1112 through 1501 )B0

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