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- PDB-6fad: SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27 -

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Basic information

Entry
Database: PDB / ID: 6fad
TitleSR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27
Components
  • SRSF protein kinase 1
  • mRNA export factor
KeywordsSPLICING / Complex / Phosphorylation / Inhibition
Function / homology
Function and homology information


: / symbiont-mediated suppression of host mRNA processing / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of viral genome replication ...: / symbiont-mediated suppression of host mRNA processing / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation / nuclear matrix / host cell cytoplasm / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / host cell nucleus / chromatin / regulation of DNA-templated transcription / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Herpes viral adaptor, REF-binding domain / Herpes viral adaptor-to-host cellular mRNA binding domain / Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / 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. ...Herpes viral adaptor, REF-binding domain / Herpes viral adaptor-to-host cellular mRNA binding domain / Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / 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
PHOSPHATE ION / mRNA export factor / mRNA export factor / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Herpes simplex virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsTunnicliffe, R.B. / Levy, C. / Mould, A.P. / Mckenzie, E.A. / Sandri-Goldin, R.M. / Golovanov, A.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI107803 United States
CitationJournal: Mbio / Year: 2019
Title: Molecular Mechanism of SR Protein Kinase 1 Inhibition by the Herpes Virus Protein ICP27.
Authors: Tunnicliffe, R.B. / Hu, W.K. / Wu, M.Y. / Levy, C. / Mould, A.P. / McKenzie, E.A. / Sandri-Goldin, R.M. / Golovanov, A.P.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SRSF protein kinase 1
B: SRSF protein kinase 1
C: SRSF protein kinase 1
D: SRSF protein kinase 1
E: mRNA export factor
F: mRNA export factor
G: mRNA export factor
H: mRNA export factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,93413
Polymers287,4598
Non-polymers4755
Water3,405189
1
A: SRSF protein kinase 1
E: mRNA export factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0554
Polymers71,8652
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SRSF protein kinase 1
H: mRNA export factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0554
Polymers71,8652
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SRSF protein kinase 1
G: mRNA export factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9603
Polymers71,8652
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SRSF protein kinase 1
F: mRNA export factor


Theoretical massNumber of molelcules
Total (without water)71,8652
Polymers71,8652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.980, 99.980, 426.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein
SRSF protein kinase 1 / SFRS protein kinase 1 / Serine/arginine-rich protein-specific kinase 1 / SR-protein-specific kinase 1


Mass: 70118.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Truncated construct SRPK1dNS1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RP
References: UniProt: Q96SB4, non-specific serine/threonine protein kinase
#2: Protein/peptide
mRNA export factor / Immediate-early protein IE63 / Infected cell protein 27 / ICP27


Mass: 1746.006 Da / Num. of mol.: 4 / Fragment: ICP27 residues 137-152 / Source method: obtained synthetically / Source: (synth.) Herpes simplex virus (type 1 / strain 17) / References: UniProt: P36295, UniProt: P10238*PLUS
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 42.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09 M (Sodium nitrate, 0.3 Sodium phosphate, 0.3 M ammonium sulphate), 0.1 M (Sodium HEPES, MOPS) buffer system, 50% v/v GOL_P4K mix [Morpheus HT96 C7, Molecular Dimensions]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.801→80.21 Å / Num. obs: 60695 / % possible obs: 99.95 % / Observed criterion σ(F): 1.36 / Redundancy: 10.1 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0953 / Rpim(I) all: 0.03136 / Rrim(I) all: 0.1004 / Net I/σ(I): 17.5
Reflection shellResolution: 2.801→2.901 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.7533 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 5993 / CC1/2: 0.812 / Rpim(I) all: 0.2681 / Rrim(I) all: 0.8004 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAK

1wak


Resolution: 2.801→80.21 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2993 4.93 %Random selection
Rwork0.1979 ---
obs0.2009 60672 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→80.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11885 0 25 189 12099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812192
X-RAY DIFFRACTIONf_angle_d0.96616471
X-RAY DIFFRACTIONf_dihedral_angle_d12.3137264
X-RAY DIFFRACTIONf_chiral_restr0.0561784
X-RAY DIFFRACTIONf_plane_restr0.0062078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8008-2.84670.34311360.25362759X-RAY DIFFRACTION100
2.8467-2.89580.31881510.23332647X-RAY DIFFRACTION100
2.8958-2.94850.30191690.23322740X-RAY DIFFRACTION100
2.9485-3.00520.27791350.22462714X-RAY DIFFRACTION100
3.0052-3.06650.32761260.23582706X-RAY DIFFRACTION100
3.0665-3.13320.32051310.24312778X-RAY DIFFRACTION100
3.1332-3.20610.34181280.24152701X-RAY DIFFRACTION100
3.2061-3.28630.31571290.23032722X-RAY DIFFRACTION100
3.2863-3.37510.2841680.21732714X-RAY DIFFRACTION100
3.3751-3.47450.2971340.21452748X-RAY DIFFRACTION100
3.4745-3.58660.26611350.2112758X-RAY DIFFRACTION100
3.5866-3.71480.23721380.20372744X-RAY DIFFRACTION100
3.7148-3.86350.22811480.18742734X-RAY DIFFRACTION100
3.8635-4.03930.22721450.17142719X-RAY DIFFRACTION100
4.0393-4.25230.22751650.17042720X-RAY DIFFRACTION100
4.2523-4.51870.21451270.16122775X-RAY DIFFRACTION100
4.5187-4.86750.2021460.15672737X-RAY DIFFRACTION100
4.8675-5.35730.23521560.16582758X-RAY DIFFRACTION100
5.3573-6.13230.27131350.18992801X-RAY DIFFRACTION100
6.1323-7.7250.27011400.19032823X-RAY DIFFRACTION100
7.725-80.24540.17951510.17412881X-RAY DIFFRACTION99
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)
10.35790.083-0.03660.08480.02830.02550.01040.00470.202-0.0314-0.01360.0711-0.0436-0.1397-0.31480.0667-0.05850.03080.6047-0.06090.194120.7898-16.466314.2076
20.3743-0.0502-0.0510.0076-0.0050.05580.0442-0.00370.20180.0084-0.027-0.052-0.06820.199-0.23530.0834-0.07070.05760.6849-0.17070.242155.4711-9.359850.9348
30.3941-0.0864-0.04150.12080.04140.0808-0.0344-0.1492-0.07740.0729-0.05880.12090.0993-0.1674-0.5360.1264-0.09540.02860.807-0.02940.17319.2252-36.55752.6179
40.0158-0.02130.01440.0307-0.01830.016-0.0009-0.0523-0.0463-0.01120.0322-0.05910.10480.1104-0.07490.1032-0.0372-0.01490.6601-0.07170.172457.3102-42.092622.6176
50.00230.0018-0.0010.002-00.0012-0.00860.0019-0.0053-0.0081-0.00820.0065-0.01840.001700.3006-0.12410.12990.377-0.00110.300637.1168-11.3416-6.7668
60.0010.00040.00050.00020.00010.00070.00370.0056-0.0062-0.00150.0047-0.0010.00240.0052-00.3928-0.0556-0.00550.3544-0.01070.356643.8088-60.042310.9184
70.0029-0.0001-0.00010-0.00030.00130.0011-0.00290.00520.00650.0062-0.002-0.0018-0.001500.54690.0246-0.01150.56190.05140.44532.7019-49.368269.6534
80.00190.0003-0.00040.0003-00.00060.00380.00450.00540.0021-0.0023-0.0028-0.0045-0.0012-00.38970.00670.02330.4472-0.07460.468140.98555.264764.0991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 55 through 655)
2X-RAY DIFFRACTION2(chain 'B' and resid 55 through 655)
3X-RAY DIFFRACTION3(chain 'C' and resid 55 through 655)
4X-RAY DIFFRACTION4(chain 'D' and resid 55 through 655)
5X-RAY DIFFRACTION5(chain 'E' and resid 138 through 149)
6X-RAY DIFFRACTION6(chain 'F' and resid 142 through 148)
7X-RAY DIFFRACTION7(chain 'G' and resid 142 through 149)
8X-RAY DIFFRACTION8(chain 'H' and resid 142 through 149)

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