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- PDB-4nw2: Tandem chromodomains of human CHD1 in complex with Influenza viru... -

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Basic information

Entry
Database: PDB / ID: 4nw2
TitleTandem chromodomains of human CHD1 in complex with Influenza virus NS1 C-terminal tail trimethylated at K229
Components
  • Chromodomain-helicase-DNA-binding protein 1
  • Nonstructural protein 1
KeywordsPEPTIDE BINDING PROTEIN/VIRAL PROTEIN / Structural Genomics Consortium / SGC / PEPTIDE BINDING PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / nucleosome organization / protein serine/threonine kinase inhibitor activity / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity ...symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / nucleosome organization / protein serine/threonine kinase inhibitor activity / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / methylated histone binding / helicase activity / double-stranded RNA binding / histone binding / DNA helicase / Estrogen-dependent gene expression / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin remodeling / virus-mediated perturbation of host defense response / chromatin binding / host cell nucleus / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein 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 / 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 ...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 / 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 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / 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 / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsQin, S. / Tempel, W. / Xu, C. / El Bakkouri, M. / Bountra, C. / Arrowsmith, C.H. / 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 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 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 / 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 / _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
C: Chromodomain-helicase-DNA-binding protein 1
D: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,73837
Polymers49,5534
Non-polymers18433
Water2,900161
1
A: Chromodomain-helicase-DNA-binding protein 1
B: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,86921
Polymers24,7772
Non-polymers9219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area11480 Å2
MethodPISA
2
C: Chromodomain-helicase-DNA-binding protein 1
D: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,86916
Polymers24,7772
Non-polymers9214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-5 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.557, 92.248, 110.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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
#2: Protein/peptide Nonstructural protein 1


Mass: 1834.303 Da / Num. of mol.: 2 / Fragment: UNP residues 216-230 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: T2F8K6, UniProt: P03495*PLUS
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG8000, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.9→70.694 Å / Num. obs: 39818 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shell

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

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.9-1.943.71.7186202559100
9.11-47.253.636.4247442898.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.12data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.12data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2b2w

2b2w


Resolution: 1.9→42.968 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7981 / SU ML: 0.26 / σ(F): 0.12 / Phase error: 26.09 / Stereochemistry target values: ML
Details: REFMAC WAS USED DURING INTERMEDIATE REFINEMENT STAGES. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER. ELECTRON DENSITY FOR THE BACKBONE ...Details: REFMAC WAS USED DURING INTERMEDIATE REFINEMENT STAGES. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER. ELECTRON DENSITY FOR THE BACKBONE OF THE PEPTIDE LIGAND IS NOT CONTINUOUS. IT IS THEREFORE POSSIBLE THAT THE PEPTIDE'S AMINO-TERMINUS IS MODELED IN A DIFFERENT ASYMMETRIC UNIT RELATIVE TO THE CARBOXY-TERMINUS. WEAK ELECTRON DENSITY NEAR P417 OF EITHER CHD1 CHAIN FAINTLY RESEMBLES A PEPTIDE.
RfactorNum. reflection% reflection
Rfree0.2424 4622 6.15 %
Rwork0.1991 --
obs0.2014 39818 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.87 Å2 / Biso mean: 39.8335 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 43 161 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063031
X-RAY DIFFRACTIONf_angle_d0.8854112
X-RAY DIFFRACTIONf_chiral_restr0.037427
X-RAY DIFFRACTIONf_plane_restr0.004527
X-RAY DIFFRACTIONf_dihedral_angle_d13.5091087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Num. reflection all
1.9-1.92160.36912519100
1.9216-1.94429550.331115661002521
1.9442-1.96792940.294122491002543
1.9679-1.99280.28122444100
1.9928-2.0190.27212481100
2.019-2.04670.2682549100
2.0467-2.07590.25652478100
2.0759-2.1069140.252624991002513
2.1069-2.139810190.242614691002488
2.1398-2.17490.23042495100
2.1749-2.21240.23422520100
2.2124-2.25270.24072524100
2.2527-2.2960.22632508100
2.296-2.34284650.214420331002498
2.3428-2.39380.2032489100
2.3938-2.44952540.188422871002541
2.4495-2.51070.20342475100
2.5107-2.57862190.200123001002519
2.5786-2.65450.20252513100
2.6545-2.74012170.20222811002498
2.7401-2.8380.20372502100
2.838-2.95162070.193222881002495
2.9516-3.08591790.193623411002520
3.0859-3.24860.18512531100
3.2486-3.4521540.181323551002509
3.452-3.71841360.175423681002504
3.7184-4.0924970.156523881002485
4.0924-4.68391590.158123431002502
4.6839-5.89881230.178423891002512
5.8988-42.97891300.20262355992485
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)
12.1798-0.9138-0.92582.37630.74982.93220.04960.1178-0.08870.0335-0.11210.2964-0.1695-0.111-0.02980.2105-0.0363-0.01650.2431-0.00740.244112.3207-13.8053-14.2754
20.13610.12840.02490.14640.0450.0318-0.37740.2976-0.29170.0161-0.31330.19950.4003-0.3197-0.00060.6087-0.1158-0.2450.5105-0.0030.898843.5802-8.6703-14.8438
30.0445-0.03060.04980.0439-0.00780.05140.2997-0.32610.04490.46190.0958-0.49460.33620.1253-0.00070.3832-0.0059-0.07840.6993-0.08910.405225.7606-16.7655-10.0106
42.23081.2515-1.36611.948-0.44252.41570.1295-0.17630.093-0.0152-0.0599-0.1073-0.34780.19050.00370.2722-0.00090.00310.2391-0.01670.2382-9.787-14.1633-40.6453
50.0035-0.01090.00540.0020.0007-0.0031-0.2226-0.1932-0.26720.0025-0.0736-0.23880.31570.396-0.00090.72050.0051-0.15630.6251-0.00760.7848-40.7427-9.7465-39.9999
60.0288-0.01420.02190.03410.01550.03870.07450.3021-0.0666-0.2701-0.14030.78090.2606-0.1201-0.00220.4591-0.0071-0.01270.65710.06780.4485-23.6295-16.8832-45.0683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA270 - 442
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 216:220B216 - 220
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 224:230B224 - 230
4X-RAY DIFFRACTION4CHAIN CC270 - 442
5X-RAY DIFFRACTION5CHAIN D AND RESSEQ 216:221D216 - 221
6X-RAY DIFFRACTION6CHAIN D AND RESSEQ 224:230D224 - 230

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