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- PDB-7e2k: Crystal structure of the RWD domain of human GCN2 - 1 -

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Basic information

Entry
Database: PDB / ID: 7e2k
TitleCrystal structure of the RWD domain of human GCN2 - 1
ComponentseIF-2-alpha kinase GCN2
KeywordsTRANSFERASE / Activator / Kinase / RNA-binding / Serine/threonine-protein kinase / tRNA-binding
Function / homology
Function and homology information


positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / negative regulation by host of viral genome replication / regulation of feeding behavior ...positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / negative regulation by host of viral genome replication / regulation of feeding behavior / T cell activation involved in immune response / positive regulation of adaptive immune response / regulation of translational initiation / cellular response to cold / neuron projection extension / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of neuron differentiation / long-term memory / negative regulation of translational initiation / positive regulation of defense response to virus by host / cellular response to amino acid starvation / cytosolic ribosome / DNA damage checkpoint signaling / learning / positive regulation of long-term synaptic potentiation / cellular response to UV / viral translation / defense response to virus / tRNA binding / protein autophosphorylation / adaptive immune response / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 Å
AuthorsHei, Z. / Zhou, J. / Liu, Z. / Wang, J. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structures reveal a novel dimer of the RWD domain of human general control nonderepressible 2.
Authors: Hei, Z. / Wu, S. / Zheng, L. / Zhou, J. / Liu, Z. / Wang, J. / Fang, P.
History
DepositionFeb 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: eIF-2-alpha kinase GCN2


Theoretical massNumber of molelcules
Total (without water)15,3011
Polymers15,3011
Non-polymers00
Water1,35175
1
A: eIF-2-alpha kinase GCN2

A: eIF-2-alpha kinase GCN2


Theoretical massNumber of molelcules
Total (without water)30,6022
Polymers30,6022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2350 Å2
ΔGint-16 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.370, 110.370, 110.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein eIF-2-alpha kinase GCN2 / Eukaryotic translation initiation factor 2-alpha kinase 4 / GCN2-like protein


Mass: 15301.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK4, GCN2, KIAA1338 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P2K8, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.66 Å3/Da / Density % sol: 66.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.04→45.06 Å / Num. obs: 27621 / % possible obs: 100 % / Redundancy: 21.4 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.031 / Rrim(I) all: 0.14 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.04-2.0922.91.5952421410560.6630.341.6312.3100
9.13-45.0617.50.05732921880.9990.0140.05940.899.5

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UKX

1ukx


Resolution: 2.041→45.058 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.27 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1466 5.31 %
Rwork0.2154 26155 -
obs0.2164 27621 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.48 Å2 / Biso mean: 42.4102 Å2 / Biso min: 28.25 Å2
Refinement stepCycle: final / Resolution: 2.041→45.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 75 1034
Biso mean---53.06 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0411-2.1140.31421280.31842666
2.114-2.19870.30121200.29092616
2.1987-2.29870.32131420.31362646
2.2987-2.41990.35761450.29632574
2.4199-2.57150.30121760.28552602
2.5715-2.77010.20871520.22922598
2.7701-3.04880.19681520.20912610
3.0488-3.48980.22111440.19742604
3.4898-4.39620.18061600.1732604
4.3962-45.0580.2391470.19232635
Refinement TLS params.Method: refined / Origin x: 17.048 Å / Origin y: 48.692 Å / Origin z: 7.2085 Å
111213212223313233
T0.2176 Å2-0.0048 Å2-0.0112 Å2-0.294 Å2-0.0111 Å2--0.2406 Å2
L2.544 °2-0.2875 °2-0.7687 °2-1.8305 °2-0.1517 °2--2.3398 °2
S-0.0105 Å °-0.0562 Å °-0.0938 Å °-0.077 Å °0.0251 Å °-0.0414 Å °0.0136 Å °-0.1416 Å °0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 138
2X-RAY DIFFRACTION1allS1 - 78

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