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- PDB-4o42: Tandem chromodomains of human CHD1 in complex with influenza NS1 ... -

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Basic information

Entry
Database: PDB / ID: 4o42
TitleTandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229
Components
  • Chromodomain-helicase-DNA-binding protein 1
  • Nonstructural protein 1
KeywordsDNA BINDING PROTEIN/VIRAL PROTEIN / viral / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / : / nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / : / nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / histone binding / Estrogen-dependent gene expression / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin remodeling / symbiont-mediated suppression of host gene expression / chromatin binding / chromatin / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / helicase superfamily c-terminal domain / S15/NS1, RNA-binding / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / 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 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 20, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 1
B: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,85414
Polymers24,7622
Non-polymers9212
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.068, 46.057, 46.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1 / ATP-dependent helicase CHD1


Mass: 22942.408 Da / Num. of mol.: 1 / Fragment: UNP residues 268-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: O14646, DNA helicase
#2: Protein/peptide Nonstructural protein 1


Mass: 1819.269 Da / Num. of mol.: 1 / Fragment: UNP residues 216-230 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Influenza A virus / References: UniProt: Q38SQ2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.8 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 291 K / pH: 7
Details: 15% PEG3350, 0.1 succinic acid, pH 7, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→46.06 Å / Num. obs: 20229 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.87-1.917.31.692821276100
8.97-46.065.531.9128823398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B2W

2b2w


Resolution: 1.87→46.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2131 / WRfactor Rwork: 0.1825 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8353 / SU B: 6.096 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1249 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: coot was used for interactive model building. Model geometry was assessed with molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 997 4.9 %RANDOM
Rwork0.1889 ---
obs0.1905 20188 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.25 Å2 / Biso mean: 41.1586 Å2 / Biso min: 17.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-0 Å2
2--1.81 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 17 96 1528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021495
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9252033
X-RAY DIFFRACTIONr_angle_other_deg0.83633062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61924.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05915240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.059157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_mcbond_it2.5962.416728
X-RAY DIFFRACTIONr_mcbond_other2.5782.411727
X-RAY DIFFRACTIONr_mcangle_it3.5053.598909
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 84 -
Rwork0.279 1396 -
all-1480 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.2516 Å / Origin y: -12.1436 Å / Origin z: 14.2216 Å
111213212223313233
T0.0397 Å20.0174 Å2-0.0149 Å2-0.0904 Å2-0.0188 Å2--0.0254 Å2
L2.8349 °21.3715 °21.3507 °2-1.9098 °21.2134 °2--3.4712 °2
S0.097 Å °0.2592 Å °-0.2584 Å °-0.0122 Å °0.0887 Å °-0.132 Å °0.3123 Å °0.1271 Å °-0.1857 Å °

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