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- PDB-1kl9: Crystal structure of the N-terminal segment of Human eukaryotic i... -

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Basic information

Entry
Database: PDB / ID: 1kl9
TitleCrystal structure of the N-terminal segment of Human eukaryotic initiation factor 2alpha
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
KeywordsTRANSLATION / OB FOLD / HELICAL DOMAIN
Function / homology
Function and homology information


translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP ...translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / mitophagy / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / response to endoplasmic reticulum stress / translational initiation / PKR-mediated signaling / ABC-family proteins mediated transport / cytoplasmic stress granule / cellular response to UV / ribosome binding / cellular response to heat / cellular response to oxidative stress / synapse / mitochondrion / RNA binding / extracellular exosome / nucleus / membrane / cytosol
Similarity search - Function
Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain ...Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsNonato, M.C. / Widom, J. / Clardy, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2alpha
Authors: Nonato, M.C. / Widom, J. / Clardy, J.
History
DepositionDec 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7015
Polymers21,4391
Non-polymers2624
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
hetero molecules

A: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,40110
Polymers42,8782
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2420 Å2
ΔGint-262 kcal/mol
Surface area15770 Å2
MethodPISA, PQS
3
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
hetero molecules

A: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,40110
Polymers42,8782
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1350 Å2
ΔGint-169 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.280, 44.200, 121.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Cell settingorthorhombic
Space group name H-MP2221

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 / Eukaryotic translation initiation factor 2 alpha subunit / eIF-2-alpha / EIF-2alpha / EIF-2A


Mass: 21439.061 Da / Num. of mol.: 1 / Fragment: residues 1-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05198
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, sodium acetate, zinc chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP at 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
210-16 %PEG40001reservoir
3100 mMsodium acetate1reservoir
40.2 M1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795, 0.9793, 0.9640
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 27, 2000
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.9641
ReflectionResolution: 1.9→60 Å / Num. obs: 14922 / % possible obs: 90.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23264 723 4.9 %RANDOM
Rwork0.19802 ---
all0.199 ---
obs0.19969 14172 90.2 %-
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 4 94 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it8.1570
X-RAY DIFFRACTIONp_mcangle_it10.5810
X-RAY DIFFRACTIONp_scbond_it22.1860
X-RAY DIFFRACTIONp_scangle_it27.9750
X-RAY DIFFRACTIONp_bond_d0.0160.021
X-RAY DIFFRACTIONp_angle_deg1.1991.949
X-RAY DIFFRACTIONp_angle_d1.1991.949
X-RAY DIFFRACTIONp_planar_d0.0050.02
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.0650.2
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1710.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 3 / % reflection Rfree: 4.9 % / Rfactor all: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.19

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