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- PDB-3lq9: Crystal structure of human REDD1, a hypoxia-induced regulator of mTOR -

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Basic information

Entry
Database: PDB / ID: 3lq9
TitleCrystal structure of human REDD1, a hypoxia-induced regulator of mTOR
ComponentsDNA-damage-inducible transcript 4 protein
KeywordsSIGNALING PROTEIN / REDD1 DDIT4 mTOR / hypoxia / cancer
Function / homology
Function and homology information


protein-containing complex disassembly / negative regulation of glycolytic process / negative regulation of TOR signaling / neurotrophin TRK receptor signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 14-3-3 protein binding / reactive oxygen species metabolic process / cellular response to dexamethasone stimulus / TP53 Regulates Metabolic Genes / neuron migration ...protein-containing complex disassembly / negative regulation of glycolytic process / negative regulation of TOR signaling / neurotrophin TRK receptor signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 14-3-3 protein binding / reactive oxygen species metabolic process / cellular response to dexamethasone stimulus / TP53 Regulates Metabolic Genes / neuron migration / brain development / neuron differentiation / defense response to virus / response to hypoxia / intracellular signal transduction / apoptotic process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
RTP801-like / RTP801-like / RTP801-like, C-terminal domain superfamily / RTP801 C-terminal region / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA damage-inducible transcript 4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsVega-Rubin-de-Celis, S. / Abdallah, Z. / Brugarolas, J. / Zhang, X.
CitationJournal: Biochemistry / Year: 2010
Title: Structural analysis and functional implications of the negative mTORC1 regulator REDD1.
Authors: Vega-Rubin-de-Celis, S. / Abdallah, Z. / Kinch, L. / Grishin, N.V. / Brugarolas, J. / Zhang, X.
History
DepositionFeb 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-damage-inducible transcript 4 protein
B: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)29,6622
Polymers29,6622
Non-polymers00
Water3,657203
1
A: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)14,8311
Polymers14,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)14,8311
Polymers14,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.331, 36.586, 47.970
Angle α, β, γ (deg.)77.56, 89.08, 86.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA-damage-inducible transcript 4 protein / Protein regulated in development and DNA damage response 1 / REDD-1 / HIF-1 responsive protein RTP801


Mass: 14830.898 Da / Num. of mol.: 2 / Fragment: C-terminal functional domain / Mutation: deletion of residues 200-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDIT4, REDD1, RTP801 / Plasmid: modified pET28 with a His6-Sumo tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NX09
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaF, 20-26% PEG3350, 0.05 mM C12E9, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97926
SYNCHROTRONAPS 19-BM21.28288
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJan 1, 2008
CUSTOM-MADE2CCDJan 1, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
21.282881
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 25.34 / Number: 55284 / Rmerge(I) obs: 0.079 / Χ2: 1.93 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 11682 / % possible obs: 96
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745097.110.0653.9134.9
3.764.7497.810.0552.6044.9
3.293.7698.510.0672.3075
2.993.2998.110.0861.9095
2.772.9997.810.111.5855
2.612.7797.710.1421.5175
2.482.6197.210.1561.314.8
2.372.4895.910.1721.274.6
2.282.3792.910.2051.2294.1
2.22.2887.210.2321.1153.9
ReflectionResolution: 2→50 Å / Num. obs: 14319 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 1.859 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.40.25913922.251,292.5
2.07-2.153.80.21413781.7681,294
2.15-2.253.90.15914131.6591,294.9
2.25-2.3740.13114351.7861,295.5
2.37-2.524.10.10914381.661,296.3
2.52-2.714.10.09614451.811,296.7
2.71-2.994.20.0814652.0051,296.9
2.99-3.424.20.06414452.0911,297.8
3.42-4.314.10.0514551.7971,297.7
4.31-5040.04514531.8051,297

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.096 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / SU ML: 0.28 / σ(F): 1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.214 708 5.07 %
Rwork0.177 --
obs0.179 13975 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.587 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 90.6 Å2 / Biso mean: 30.4 Å2 / Biso min: 11.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.806 Å21.177 Å21.635 Å2
2--6.712 Å2-1.821 Å2
3----2.906 Å2
Refinement stepCycle: LAST / Resolution: 2→27.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 203 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031942
X-RAY DIFFRACTIONf_angle_d0.772618
X-RAY DIFFRACTIONf_chiral_restr0.051319
X-RAY DIFFRACTIONf_plane_restr0.002332
X-RAY DIFFRACTIONf_dihedral_angle_d15.69733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1530.2611250.1982441256686
2.153-2.370.2151380.1772641277993
2.37-2.7120.2311420.182678282095
2.712-3.4160.251430.1792756289997
3.416-27.0980.1791600.1682751291197

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