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- PDB-2l75: Solution structure of CHD4-PHD2 in complex with H3K9me3 -

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Basic information

Entry
Database: PDB / ID: 2l75
TitleSolution structure of CHD4-PHD2 in complex with H3K9me3
Components
  • 14-meric peptide from 1Histone H3.1
  • Chromodomain-helicase-DNA-binding protein 4
KeywordsTranscription/Nuclear protein / CHD4 / Mi2b / PHD2 / H3K9me3 / Transcription-Nuclear protein complex
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / Regulation of TP53 Activity through Acetylation / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / helicase activity / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / transcription coregulator binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / 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 / extracellular exosome / extracellular region / 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 / Histone H3 signature 1. / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / 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
Histone H3.1 / 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
DepositionDec 2, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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_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
B: 14-meric peptide from 1Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3914
Polymers8,2612
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: 6689.790 Da / Num. of mol.: 1 / Fragment: PHD2 domain, UNP residues 446-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: A modified version of pGEX-2T containing a HRV protease cleavage site.
Gene: CHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14839
#2: Protein/peptide 14-meric peptide from 1Histone H3.1


Mass: 1570.793 Da / Num. of mol.: 1 / Fragment: UNP residues 2-14 / Source method: obtained synthetically / Details: chemical synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE C-TERMINAL TYR OF H3K9ME3 IS NON-NATIVE, AND WAS ADDED TO ASSIST IN PEPTIDE CONCENTRATION ...THE C-TERMINAL TYR OF H3K9ME3 IS NON-NATIVE, AND WAS ADDED TO ASSIST IN PEPTIDE CONCENTRATION DETERMINATION BY A280.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1523D HNCA
1623D CBCA(CO)NH
1723D HNHA
1823D HBHA(CO)NH
1923D HNCO
11023D HN(CA)CO
11133D (H)CCH-TOCSY
11223D CC(CO)NH TOCSY
11322D-His HSQC
1142(HB)CB(CGCD)HD
1152(HB)CB(CGCDCE)HE
11623D 1H-15N NOESY
11723D 1H-15N TOCSY
11812D 1H-1H NOESY
11933D 1H-13C NOESY
120215N-13C DHF NOESY
121313C-13C DHF NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM CHD4-PHD2-1; 1 mM H3K9me3-2, 20 uM DSS-3; 1 mM DTT-4; 5 mM sodium chloride-5; 10 mM sodium phosphate-6; 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-7; 1.1 mM H3K9me3-8; 20 uM DSS-9; 1 mM DTT-10; 5 mM sodium chloride-11; 10 mM sodium phosphate-12; 93% H2O/7% D2O93% H2O/7% D2O
31 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-13; 1.1 mM H3K9me3-14; 20 uM DSS-15; 1 mM DTT-16; 5 mM sodium chloride-17; 10 mM sodium phosphate-18; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCHD4-PHD2-11
1 mMH3K9me3-21
20 uMDSS-31
1 mMDTT-41
5 mMsodium chloride-51
10 mMsodium phosphate-61
1 mMCHD4-PHD2-7[U-100% 13C; U-100% 15N]2
1.1 mMH3K9me3-82
20 uMDSS-92
1 mMDTT-102
5 mMsodium chloride-112
10 mMsodium phosphate-122
1 mMCHD4-PHD2-13[U-100% 13C; U-100% 15N]3
1.1 mMH3K9me3-143
20 uMDSS-153
1 mMDTT-163
5 mMsodium chloride-173
10 mMsodium phosphate-183
Sample conditionsIonic strength: 15 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichintermolecular distance calibration
ARIALinge, O'Donoghue and Nilgesstructure solution
ProcheckNMRLaskowski and MacArthurrefinement and validation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
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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