[English] 日本語
Yorodumi
- PDB-6d3l: Crystal structure of unphosphorylated human PKR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d3l
TitleCrystal structure of unphosphorylated human PKR
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsTRANSFERASE / unphosphorylated / kinase / activation loop swapping / apo
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / antiviral innate immune response / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / 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 / positive regulation of non-canonical NF-kappaB signal transduction / Interferon alpha/beta signaling / double-stranded RNA 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
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsErlandsen, H. / Mayo, C. / Robinson, V.L. / Cole, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI053615 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis of Protein Kinase R Autophosphorylation.
Authors: Mayo, C.B. / Erlandsen, H. / Mouser, D.J. / Feinstein, A.G. / Robinson, V.L. / May, E.R. / Cole, J.L.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)37,4461
Polymers37,4461
Non-polymers00
Water00
1
A: Interferon-induced, double-stranded RNA-activated protein kinase

A: Interferon-induced, double-stranded RNA-activated protein kinase


  • defined by author
  • Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of ...Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of Molecular Biology, 345(1), 81-90. http://doi.org/10.1016/j.jmb.2004.10.031
  • 74.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)74,8922
Polymers74,8922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
2
A: Interferon-induced, double-stranded RNA-activated protein kinase

A: Interferon-induced, double-stranded RNA-activated protein kinase


  • defined by author
  • Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of ...Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of Molecular Biology, 345(1), 81-90. http://doi.org/10.1016/j.jmb.2004.10.031, fluorescence resonance energy transfer, Husain, B., Hesler, S., & Cole, J. L. (2015). Regulation of PKR by RNA: Formation of Active and Inactive Dimers. Biochemistry, 54(44), 6663-6672. http://doi.org/10.1021/acs.biochem.5b01046
  • 74.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)74,8922
Polymers74,8922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)92.689, 92.689, 123.325
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon- ...Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon-inducible RNA-dependent protein kinase / P1/eIF-2A protein kinase / Protein kinase RNA-activated / Protein kinase R / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 37445.773 Da / Num. of mol.: 1 / Fragment: kinase domain (229-551)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2, PKR, PRKR / Production host: Escherichia coli (E. coli)
References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 2.0 M ammonium sulfate, 1:3 molar ratio of dp8 (heparin) was added to protein prior to crystallization

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.978971 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978971 Å / Relative weight: 1
ReflectionResolution: 3.1→123.33 Å / Num. obs: 6130 / % possible obs: 100 % / Redundancy: 17.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.063 / Rrim(I) all: 0.267 / Net I/σ(I): 9.1
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.133 / Num. unique obs: 1065 / CC1/2: 0.677 / Rpim(I) all: 0.263 / Rrim(I) all: 1.163 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.04 Å80.27 Å
Translation6.04 Å80.27 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.28data scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A19

2a19


Resolution: 3.1→123.33 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.812 / SU B: 34.802 / SU ML: 0.573 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.347 296 4.9 %RANDOM
Rwork0.2585 ---
obs0.2629 5801 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.27 Å2 / Biso mean: 88.324 Å2 / Biso min: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 3.1→123.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 0 2014
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192082
X-RAY DIFFRACTIONr_bond_other_d0.0020.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9692793
X-RAY DIFFRACTIONr_angle_other_deg1.01634720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.56624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1541511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
LS refinement shellResolution: 3.1→3.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 16 -
Rwork0.383 410 -
all-426 -
obs--100 %

+
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