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- PDB-4o45: WDR5 in complex with influenza NS1 C-terminal tail -

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Basic information

Entry
Database: PDB / ID: 4o45
TitleWDR5 in complex with influenza NS1 C-terminal tail
Components
  • Nonstructural protein 1
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION/RNA BINDING PROTEIN / viral / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / signaling receptor inhibitor activity ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / signaling receptor inhibitor activity / protein serine/threonine kinase inhibitor activity / Cardiogenesis / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / MLL1 complex / histone acetyltransferase complex / : / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / double-stranded RNA binding / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / host cell cytoplasm / regulation of cell cycle / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / signaling receptor binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / host cell nucleus / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / S15/NS1, RNA-binding / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / S15/NS1, RNA-binding / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Non-structural protein 1 / WD repeat-containing protein 5 / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus H3N2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsQin, S. / Xu, C. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.
Authors: Qin, S. / Liu, Y. / Tempel, W. / Eram, M.S. / Bian, C. / Liu, K. / Senisterra, G. / Crombet, L. / Vedadi, M. / Min, J.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)36,08219
Polymers36,0822
Non-polymers017
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.218, 85.830, 40.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34289.887 Da / Num. of mol.: 1 / Fragment: UNP residues 24-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P61964
#2: Protein/peptide Nonstructural protein 1


Mass: 1792.223 Da / Num. of mol.: 1 / Fragment: C-terminal residues 216-230 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Influenza A virus H3N2 / References: UniProt: Q9YP60, UniProt: P03495*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.1 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 25% PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris, pH 6.5, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.87→37.94 Å / Num. obs: 24106 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.87-1.917.21.0542.311120153599.9
8.97-37.945.50.01169.8146626697.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.12data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished crystal structure of WDR5

Resolution: 1.87→37.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1891 / WRfactor Rwork: 0.1545 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8155 / SU B: 8.529 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1462 / SU Rfree: 0.1335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: coot was used for interactive model building. Model geometry was assessed on the molprobity server. CAVEAT: There is some uncertainty about the residue number of the arginyl residue in the ...Details: coot was used for interactive model building. Model geometry was assessed on the molprobity server. CAVEAT: There is some uncertainty about the residue number of the arginyl residue in the NS1 peptide, and surrounding residues. The arginyl residue could correspond to another arginyl position in the NS1 peptide. There is a significant mismatch between model and density for WDR5 residue N-225.
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1239 5.1 %RANDOM
Rwork0.1743 ---
obs0.1763 24062 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.66 Å2 / Biso mean: 36.4632 Å2 / Biso min: 15.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å2-0 Å20 Å2
2---0.09 Å20 Å2
3---3.03 Å2
Refinement stepCycle: LAST / Resolution: 1.87→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 17 93 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192448
X-RAY DIFFRACTIONr_bond_other_d0.0020.022234
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9323349
X-RAY DIFFRACTIONr_angle_other_deg0.78535160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2872592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98915389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.631154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_mcbond_it1.7342.1731263
X-RAY DIFFRACTIONr_mcbond_other1.7292.1681262
X-RAY DIFFRACTIONr_mcangle_it2.4153.2391581
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 98 -
Rwork0.281 1656 -
all-1754 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 12.8992 Å / Origin y: 109.3749 Å / Origin z: 8.3893 Å
111213212223313233
T0.0199 Å20.0109 Å20.0099 Å2-0.0173 Å2-0.0109 Å2--0.113 Å2
L3.1077 °20.0231 °2-0.7901 °2-1.5304 °20.6585 °2--1.8195 °2
S-0.1514 Å °0.0639 Å °-0.2571 Å °0.0967 Å °0.0947 Å °-0.08 Å °0.1725 Å °0.1405 Å °0.0567 Å °

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