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- PDB-7e2m: Crystal structure of the RWD domain of human GCN2 - 2 -

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Basic information

Entry
Database: PDB / ID: 7e2m
TitleCrystal structure of the RWD domain of human GCN2 - 2
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 / cytosolic ribosome / negative regulation of translational initiation / positive regulation of defense response to virus by host / cellular response to amino acid starvation / learning / DNA damage checkpoint signaling / positive regulation of long-term synaptic potentiation / cellular response to UV / defense response to virus / adaptive immune response / viral translation / protein autophosphorylation / tRNA binding / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
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: 2.35 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
B: eIF-2-alpha kinase GCN2
C: eIF-2-alpha kinase GCN2
D: eIF-2-alpha kinase GCN2
E: eIF-2-alpha kinase GCN2
F: eIF-2-alpha kinase GCN2


Theoretical massNumber of molelcules
Total (without water)91,8076
Polymers91,8076
Non-polymers00
Water5,098283
1
A: eIF-2-alpha kinase GCN2
B: 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
Buried area2550 Å2
ΔGint-9 kcal/mol
Surface area12360 Å2
MethodPISA
2
C: eIF-2-alpha kinase GCN2
D: 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
Buried area2470 Å2
ΔGint-10 kcal/mol
Surface area12220 Å2
MethodPISA
3
E: eIF-2-alpha kinase GCN2
F: 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
Buried area2500 Å2
ΔGint-8 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.440, 158.440, 54.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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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.: 6
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


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 7.0, 20 % PEG4000, and 20 % 2-propanol

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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: 2.35→44.901 Å / Num. obs: 63134 / % possible obs: 99.3 % / Redundancy: 11.2 % / Biso Wilson estimate: 34.99 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.06 / Rrim(I) all: 0.202 / Net I/σ(I): 10.9
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
2.35-2.4110.71.3012537923760.3990.4191.3682.599.4
10.51-44.910.30.08240343910.9980.0270.0861896

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PDB_EXTRACT3.27data extraction
PHENIX1.13refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E2K

7e2k


Resolution: 2.35→44.901 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 3019 4.78 %
Rwork0.2345 60115 -
obs0.2358 63134 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.52 Å2 / Biso mean: 37.0023 Å2 / Biso min: 20.05 Å2
Refinement stepCycle: final / Resolution: 2.35→44.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 0 283 6226
Biso mean---44.02 -
Num. residues----775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.4340.42392980.3967606599
2.434-2.53140.38362600.3902597898
2.5314-2.64660.33662880.31876031100
2.6466-2.78620.30483080.2687603699
2.7862-2.96070.28393180.25366044100
2.9607-3.18920.27393270.23116021100
3.1892-3.51010.25262870.21066063100
3.5101-4.01770.22613170.1907592898
4.0177-5.06080.21063180.18376066100
5.0608-44.9010.22892980.2133588397
Refinement TLS params.Method: refined / Origin x: -26.1614 Å / Origin y: 45.4691 Å / Origin z: 51.0717 Å
111213212223313233
T0.2883 Å20.0189 Å2-0.0054 Å2-0.2464 Å20.0033 Å2--0.2257 Å2
L0.2748 °20.008 °2-0.0118 °2-0.2239 °2-0.0043 °2--0.0723 °2
S-0.0324 Å °-0.033 Å °-0.0002 Å °0.0123 Å °-0.0097 Å °-0.0012 Å °-0.0331 Å °-0.0151 Å °0.04 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 139
2X-RAY DIFFRACTION1allB10 - 138
3X-RAY DIFFRACTION1allC10 - 138
4X-RAY DIFFRACTION1allD10 - 138
5X-RAY DIFFRACTION1allE10 - 138
6X-RAY DIFFRACTION1allF10 - 138
7X-RAY DIFFRACTION1allG1 - 305

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