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- PDB-2l5u: Structure of the first PHD finger (PHD1) from CHD4 (Mi2b) -

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Basic information

Entry
Database: PDB / ID: 2l5u
TitleStructure of the first PHD finger (PHD1) from CHD4 (Mi2b)
ComponentsChromodomain-helicase-DNA-binding protein 4
KeywordsMETAL BINDING PROTEIN / CHD4 / Mi2b / Mi2-beta / PHD / PROTEIN BINDING / peptide binding protein
Function / homology
Function and homology information


cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMansfield, R.E. / Kwan, A.H. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Plant Homeodomain (PHD) Fingers of CHD4 Are Histone H3-binding Modules with Preference for Unmodified H3K4 and Methylated H3K9
Authors: Mansfield, R.E. / Musselman, C.A. / Kwan, A.H. / Oliver, S.S. / Garske, A.L. / Davrazou, F. / Denu, J.M. / Kutateladze, T.G. / Mackay, J.P.
History
DepositionNov 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / 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 / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9833
Polymers6,8531
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 6852.672 Da / Num. of mol.: 1 / Fragment: PHD1 domain, UNP residues 365-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: pGEX-6PE is an edited version of pGEX-2T which contains an HRV3C protease cleavage site.
Gene: CHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14839
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HNCA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNHA
1813D HBHA(CO)NH
1913D HNCO
11013D HN(CA)CO
11113D (H)CCH-TOCSY
11213D HNHB
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D 1H-15N NOESY
11622D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] CHD4 PHD1-1, 10 mM sodium phosphate-2, 50 mM sodium chloride-3, 1 mM DTT-4, 20 uM DSS-5, 93% H2O/7% D2O93% H2O/7% D2O
21 mM CHD4 PHD1-6, 10 mM sodium phosphate-7, 50 mM sodium chloride-8, 1 mM DTT-9, 20 uM DSS-10, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMCHD4 PHD1-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
20 uMDSS-51
1 mMCHD4 PHD1-62
10 mMsodium phosphate-72
50 mMsodium chloride-82
1 mMDTT-92
20 uMDSS-102
Sample conditionsIonic strength: 60 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angles from chemical shifts
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Structure calculations were performed using the package ARIA1.2. Final structures are based on 988 NOE-derived distance constraints and 79 additional dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20 / Representative conformer: 1

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