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- PDB-8d4y: C-terminal SANT-SLIDE domain of human Chromodomain-helicase-DNA-b... -

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Basic information

Entry
Database: PDB / ID: 8d4y
TitleC-terminal SANT-SLIDE domain of human Chromodomain-helicase-DNA-binding protein 4 (CHD4)
ComponentsChromodomain-helicase-DNA-binding protein 4
KeywordsTRANSCRIPTION / chromodomain / SANT / SLIDE / NuRD
Function / homology
Function and homology information


cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / site of DNA damage ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / site of DNA damage / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / helicase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / transcription coregulator binding / HDACs deacetylate histones / double-strand break repair via homologous recombination / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 ...CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Helicase conserved C-terminal domain / Zinc finger, FYVE/PHD-type / helicase superfamily c-terminal domain / 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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMoghaddas Sani, H. / Deshpande, C.N. / Panjikar, S. / Patel, K. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2022
Title: The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families.
Authors: Zhong, Y. / Moghaddas Sani, H. / Paudel, B.P. / Low, J.K.K. / Silva, A.P.G. / Mueller, S. / Deshpande, C. / Panjikar, S. / Reid, X.J. / Bedward, M.J. / van Oijen, A.M. / Mackay, J.P.
History
DepositionJun 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 4
B: Chromodomain-helicase-DNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)98,5352
Polymers98,5352
Non-polymers00
Water1086
1
A: Chromodomain-helicase-DNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)49,2681
Polymers49,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chromodomain-helicase-DNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)49,2681
Polymers49,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.432, 66.665, 99.370
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 4 / CHD-4 / ATP-dependent helicase CHD4 / Mi-2 autoantigen 218 kDa protein / Mi2-beta


Mass: 49267.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14839, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1 M bicine/Trizma base pH 8.3, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M mixture of carboxylic acids*, and 20 mM spermidine *Sodium Formate; Ammonium acetate; Sodium citrate ...Details: 0.1 M bicine/Trizma base pH 8.3, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M mixture of carboxylic acids*, and 20 mM spermidine *Sodium Formate; Ammonium acetate; Sodium citrate tribasic dihydrate; Potassium sodium tartrate tetrahydrate; Sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→48.809 Å / Num. obs: 18602 / % possible obs: 98 % / Redundancy: 4.442 % / Biso Wilson estimate: 81.59 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.131 / Χ2: 0.857 / Net I/σ(I): 9.28 / Num. measured all: 82638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.074.5690.8111.7112751304427910.7060.91691.7
3.07-3.284.7120.5233.1513409285228460.8730.59199.8
3.28-3.544.3720.2685.8811569266226460.9590.30699.4
3.54-3.884.3570.1779.5810580245524280.9790.20298.9
3.88-4.334.4970.11912.919897221522010.9870.13599.4
4.33-54.2830.09214.718412197919640.9920.10499.2
5-6.114.2670.08514.917071167616570.9910.09798.9
6.11-8.574.450.07417.345807131613050.9920.08399.2
8.57-48.8094.1130.06520.2331427787640.9920.07498.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 2.9→19.9 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3012 902 4.89 %
Rwork0.2632 17542 -
obs0.265 18444 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.66 Å2 / Biso mean: 90.0746 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 0 6 3557
Biso mean---65.96 -
Num. residues----427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.080.34231380.33792751288993
3.08-3.320.3451640.341729433107100
3.32-3.650.31871460.30482934308099
3.65-4.170.30851310.26472956308799
4.17-5.240.27761770.24822928310599
5.24-19.90.29081460.22533030317699

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