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- PDB-4otm: Crystal structure of the C-terminal domain from yeast GCN2 -

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Basic information

Entry
Database: PDB / ID: 4otm
TitleCrystal structure of the C-terminal domain from yeast GCN2
ComponentsSerine/threonine-protein kinase GCN2
KeywordsTRANSFERASE / C-terminal regulatory domain / GCN2 / 4-stranded beta sheet 3 helix bundle / regulatory domain of eIF2 stress kinase
Function / homology
Function and homology information


cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / : / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity ...cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / : / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding / translation initiation factor binding / cellular response to amino acid starvation / cytosolic ribosome / DNA damage checkpoint signaling / : / ribosome binding / large ribosomal subunit / double-stranded RNA binding / small ribosomal subunit / tRNA binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / protein phosphorylation / protein serine kinase activity / protein homodimerization activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain superfamily ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsHe, H. / Georgiadis, M.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structures of GCN2 Protein Kinase C-terminal Domains Suggest Regulatory Differences in Yeast and Mammals.
Authors: He, H. / Singh, I. / Wek, S.A. / Dey, S. / Baird, T.D. / Wek, R.C. / Georgiadis, M.M.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase GCN2
B: Serine/threonine-protein kinase GCN2


Theoretical massNumber of molelcules
Total (without water)31,4112
Polymers31,4112
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-23 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.126, 118.896, 46.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serine/threonine-protein kinase GCN2


Mass: 15705.565 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AAS1, GCN2, YDR283C / Production host: Escherichia coli (E. coli) / Strain (production host): pET28
References: UniProt: P15442, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 21-28% (w/v) polyethylene glycol 2000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.00587 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00587 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18888 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 35.35 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.073 / Net I/σ(I): 23.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.982.90.267781.029181.9
1.98-2.0230.2238620.972186.9
2.02-2.063.10.2058861.143190.6
2.06-2.13.30.1919181.113193.9
2.1-2.153.30.1689731.14197.1
2.15-2.23.50.1479361.129197.7
2.2-2.253.50.1269721.118197.6
2.25-2.313.60.1169501.063198.2
2.31-2.383.60.119931.068197.9
2.38-2.463.70.0989591.1198
2.46-2.543.80.0879431.09197
2.54-2.653.80.089851.1197.9
2.65-2.774.10.0749881.057197.9
2.77-2.914.30.0629671.009197.4
2.91-3.14.60.0549661.024197.2
3.1-3.334.70.0459791.017196.6
3.33-3.674.80.049801.098196.6
3.67-4.24.90.0349691.094194.9
4.2-5.294.80.0289771.115193.1
5.29-504.70.0259071.013180.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.14data extraction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→33.138 Å / FOM work R set: 0.7813 / SU ML: 0.56 / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 975 5.17 %Random
Rwork0.2223 ---
obs0.225 18871 94.3 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.301 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 126.96 Å2 / Biso mean: 45.35 Å2 / Biso min: 21.69 Å2
Baniso -1Baniso -2Baniso -3
1-11.9542 Å2-0 Å2-0 Å2
2---9.8118 Å20 Å2
3----2.1424 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 0 109 1954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081891
X-RAY DIFFRACTIONf_angle_d1.0712560
X-RAY DIFFRACTIONf_chiral_restr0.072289
X-RAY DIFFRACTIONf_plane_restr0.004326
X-RAY DIFFRACTIONf_dihedral_angle_d16.639700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9424-2.04480.32291330.27172224235784
2.0448-2.17290.29491390.24922548268796
2.1729-2.34060.27851410.22992613275498
2.3406-2.57610.32681400.23092627276798
2.5761-2.94870.28181430.24312651279498
2.9487-3.71420.27261400.20772643278397
3.7142-33.14330.25251390.21312590272990
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)
1-0.00130.0247-0.09270.0698-0.07840.11610.22410.1068-0.5676-0.0274-0.1862-0.3930.68620.0525-0.00050.43650.0776-0.04810.3921-0.06070.445533.98.91521.206
20.8915-0.0916-0.69840.09910.05160.53010.60460.07490.0820.58450.4709-0.5389-0.51170.93170.09750.6073-0.0137-0.18160.411-0.10450.327630.56621.40233.101
322.00012.00275.3397-9.95142.0011.8939-3.38842.86831.0987-1.58881.1426-0.69132.4774-0.67040.7677-0.2871-0.6404-0.029-0.06391.509935.578.18830.215
4-0.06230.06690.00850.1196-0.19230.1509-0.24350.30770.27840.3499-0.06140.19740.26610.328-0.00010.4071-0.00070.00920.22650.04510.362427.2924.6724.145
51.7412-0.9022-0.13951.7943-0.35042.88150.1146-0.0247-0.0362-0.4165-0.06650.2327-0.3916-0.00710.00010.27690.0176-0.06050.2689-0.01360.235610.59817.3454.592
60.3037-0.1155-0.29390.06090.14820.21510.69060.4117-0.2342-0.5016-0.57810.43850.14070.6060.00110.5490.0998-0.18650.3724-0.03930.44349.00210.454-4.738
70.0499-0.04990.01690.04690.02360.02080.10980.31620.4186-0.4074-0.2337-0.1849-0.29270.4453-0.00010.82970.2351-0.21830.4799-0.17020.69757.52213.562-16.711
80.0437-0.0158-0.017-0.00080.00540.0094-0.11280.1477-0.53130.1952-0.01610.18910.06290.11130.00071.2530.1135-0.06881.0427-0.13070.674313.694.804-9.494
90.00010.003-0.00460.001-0.0113-0.01210.53960.3281-0.3307-0.16160.15260.19710.31610.17070.00240.68280.2455-0.12270.4344-0.05670.469819.9424.961-2.826
100.5562-0.1573-0.18222.17720.21121.5963-0.0901-0.02450.08110.14040.0133-0.0164-0.049-0.0013-00.2181-0.03540.00660.2797-0.03050.265526.04120.83718.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1537:1543 )A1537 - 1543
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1544:1549 )A1544 - 1549
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1559:1559 )A1559
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1560:1573 )A1560 - 1573
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1574:1659 )A1574 - 1659
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1538:1549 )B1538 - 1549
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1550:1555 )B1550 - 1555
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1560:1563 )B1560 - 1563
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1564:1570 )B1564 - 1570
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1571:1659 )B1571 - 1659

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