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- PDB-6w0l: Henipavirus W protein interacts with 14-3-3 to modulate host gene... -

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Basic information

Entry
Database: PDB / ID: 6w0l
TitleHenipavirus W protein interacts with 14-3-3 to modulate host gene expression
Components
  • 14-3-3 protein sigma
  • Phosphorylated W peptide
KeywordsPROTEIN BINDING / Complex / phosphorylation / nuclear import / nuclear localization
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / amyloid fibril formation / regulation of cell cycle / symbiont-mediated suppression of host innate immune response / cadherin binding / virus-mediated perturbation of host defense response / host cell nucleus / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
Protein W / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
Pteropus alecto (black flying fox)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsEdwards, M. / Hoad, M. / Tsimbalyuk, S. / Menicucci, A. / Messaoudi, I. / Forwood, J. / Basler, C.
CitationJournal: J.Virol. / Year: 2020
Title: Henipavirus W Proteins Interact with 14-3-3 To Modulate Host Gene Expression.
Authors: Edwards, M.R. / Hoad, M. / Tsimbalyuk, S. / Menicucci, A.R. / Messaoudi, I. / Forwood, J.K. / Basler, C.F.
History
DepositionMar 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 5, 2021Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence ...pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_auth_evidence.experimental_support / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_type.id
Revision 1.4Oct 11, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Phosphorylated W peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8733
Polymers27,8332
Non-polymers401
Water57632
1
A: 14-3-3 protein sigma
P: Phosphorylated W peptide
hetero molecules

A: 14-3-3 protein sigma
P: Phosphorylated W peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7476
Polymers55,6674
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)83.040, 112.000, 62.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Phosphorylated W peptide


Mass: 1290.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C1C7*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% PEG 400, 0.1 M HEPES pH 7.5, 0.2 M CaCl2 and 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9357 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 2.3→24.97 Å / Num. obs: 13246 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.978 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.096 / Rrim(I) all: 0.212 / Net I/σ(I): 5.2 / Num. measured all: 63050 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.384.50.698569712770.3440.370.7932.199.8
8.91-24.974.60.06811392490.9880.0360.07710.494.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAT

4dat


Resolution: 2.3→24.968 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.03
RfactorNum. reflection% reflection
Rfree0.2647 644 4.87 %
Rwork0.2102 --
obs0.2128 13233 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.02 Å2 / Biso mean: 36.2406 Å2 / Biso min: 16.36 Å2
Refinement stepCycle: final / Resolution: 2.3→24.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 1 32 1928
Biso mean--53.22 31.65 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.47750.3711300.27762466100
2.4775-2.72660.31981340.26472491100
2.7266-3.12050.28851280.2372504100
3.1205-3.9290.2781220.195251499
3.929-24.9680.19351300.1739261499

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