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- PDB-6d3k: Crystal structure of unphosphorylated human PKR kinase domain in ... -

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Basic information

Entry
Database: PDB / ID: 6d3k
TitleCrystal structure of unphosphorylated human PKR kinase domain in complex with ADP
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsTRANSFERASE / unphosphorylated / kinase / complex / activation loop swapping / dimer
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsErlandsen, H. / Mayo, C.B. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Interferon-induced, double-stranded RNA-activated protein kinase
A: Interferon-induced, double-stranded RNA-activated protein kinase
C: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,74420
Polymers112,3373
Non-polymers2,40717
Water93752
1
B: Interferon-induced, double-stranded RNA-activated protein kinase
A: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,36912
Polymers74,8922
Non-polymers1,47710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-92 kcal/mol
Surface area26270 Å2
MethodPISA
2
B: Interferon-induced, double-stranded RNA-activated protein kinase
C: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,46413
Polymers74,8922
Non-polymers1,57211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-87 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.480, 159.600, 172.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules BAC

#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.: 3 / 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

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 6% v/v PEG400, 2.0 M ammonium sulfate, protein was complexed with AMP-PNP and Mg2+ prior to crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979413 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2016
Details: Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979413 Å / Relative weight: 1
ReflectionResolution: 2.6→172.99 Å / Num. obs: 44360 / % possible obs: 97.5 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.043 / Rrim(I) all: 0.099 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.49 / Num. unique obs: 4652 / CC1/2: 0.666 / Rpim(I) all: 0.716 / Rrim(I) all: 1.661 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.31 Å88.58 Å
Translation6.31 Å88.58 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimless0.5.29data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UIU

3uiu


Resolution: 2.6→172.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.328 / SU ML: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.278 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 2245 5.1 %RANDOM
Rwork0.209 ---
obs0.212 42089 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.14 Å2 / Biso mean: 85.889 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2---5.08 Å20 Å2
3---1.55 Å2
Refinement stepCycle: final / Resolution: 2.6→172.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 139 52 6485
Biso mean--91.04 68.93 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196534
X-RAY DIFFRACTIONr_bond_other_d0.0020.026242
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9958779
X-RAY DIFFRACTIONr_angle_other_deg1.048314505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36624.305295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.489151285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7271536
X-RAY DIFFRACTIONr_chiral_restr0.0940.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021317
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 157 -
Rwork0.4 3154 -
all-3311 -
obs--98.19 %

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