[English] 日本語
Yorodumi
- PDB-2a1a: PKR kinase domain-eIF2alpha Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a1a
TitlePKR kinase domain-eIF2alpha Complex
Components
  • Eukaryotic translation initiation factor 2 alpha subunit
  • Interferon-induced, double-stranded RNA-activated protein kinase
Keywordsprotein synthesis/transferase / transferase / kinase / protein biosynthesis / protein synthesis-transferase COMPLEX
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2alpha kinase activity / ABC-family proteins mediated transport / response to interferon-alpha / eukaryotic translation initiation factor 2 complex / negative regulation of osteoblast proliferation / multi-eIF complex ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2alpha kinase activity / ABC-family proteins mediated transport / response to interferon-alpha / eukaryotic translation initiation factor 2 complex / negative regulation of osteoblast proliferation / multi-eIF complex / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of viral genome replication / antiviral innate immune response / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / translational initiation / translation initiation factor activity / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / Interferon alpha/beta signaling / double-stranded RNA binding / ribosome binding / kinase activity / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of MAPK cascade / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / translation / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor 2; subunit 1; domain 2 / EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Translation initiation factor 2; subunit 1; domain 2 / EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2 subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDar, A.C. / Dever, T.E. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Higher-Order Substrate Recognition of eIF2alpha by the RNA-Dependent Protein Kinase PKR.
Authors: Dar, A.C. / Dever, T.E. / Sicheri, F.
History
DepositionJun 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2 alpha subunit
B: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)53,3532
Polymers53,3532
Non-polymers00
Water27015
1
A: Eukaryotic translation initiation factor 2 alpha subunit
B: Interferon-induced, double-stranded RNA-activated protein kinase

A: Eukaryotic translation initiation factor 2 alpha subunit
B: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)106,7074
Polymers106,7074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_794x-y+2,-y+4,-z-2/31
Unit cell
Length a, b, c (Å)84.300, 84.300, 165.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Eukaryotic translation initiation factor 2 alpha subunit / eIF-2- alpha


Mass: 20553.781 Da / Num. of mol.: 1 / Mutation: residue 258-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUI2, TIF211 / Plasmid: modified pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P20459
#2: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Interferon-inducible RNA-dependent protein kinase / p68 kinase / P1/eIF-2A protein kinase


Mass: 32799.551 Da / Num. of mol.: 1 / Mutation: residue 3-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKR, EIF2AK2, PKR / Plasmid: modified pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P19525, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growpH: 8 / Details: pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 17397 / % possible obs: 99.5 % / Rsym value: 0.057 / Net I/σ(I): 24.3
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.454 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q46 for chain A and a PKR homology model (based on PDB entries 2CPK, 1BKX, 1FMO, 1ATP and 1BX6 for chain B.

1q46

2cpk

1bkx

1fmo

1atp

1bx6


Resolution: 2.8→29.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.651 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.206 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26837 1662 10 %RANDOM
Rwork0.2067 ---
obs0.21286 14967 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.17 Å20 Å2
2---0.35 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 0 15 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9754788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12924.39164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.21215702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22390
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.52200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98723454
X-RAY DIFFRACTIONr_scbond_it1.22831540
X-RAY DIFFRACTIONr_scangle_it2.0724.51334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 115 -
Rwork0.317 944 -
obs--87.23 %
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)
14.0190.08021.05183.38061.89395.65330.23060.0444-0.30380.0201-0.0830.10690.1991-0.2201-0.14750.03130.0269-0.05950.02870.0304-0.204743.68597.824-88.831
22.0919-1.3358-0.52843.46871.05032.159-0.0718-0.0965-0.16790.32120.2526-0.54190.43840.3095-0.18070.1666-0.0017-0.09570.1028-0.08-0.175449.843126.814-57.378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1753 - 175
2X-RAY DIFFRACTION1AC176 - 1831 - 8
3X-RAY DIFFRACTION2BB255 - 5411 - 274
4X-RAY DIFFRACTION2BD9 - 151 - 7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more