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- PDB-2b2w: Tandem chromodomains of human CHD1 complexed with Histone H3 Tail... -

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Basic information

Entry
Database: PDB / ID: 2b2w
TitleTandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4
Components
  • (Chromodomain-helicase-DNA-binding protein 1) x 2
  • Histone H3
KeywordsPEPTIDE BINDING PROTEIN / CHD / Chromodomain / three stranded antiparallel Beta sheet / alpha helix linker / histone H3 / trimethyllysine
Function / homology
Function and homology information


nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression ...nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / helicase activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / chromatin / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / 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 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...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 / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 1 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFlanagan IV, J.F. / Mi, L.-Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S.
CitationJournal: Nature / Year: 2005
Title: Double chromodomains cooperate to recognize the methylated histone H3 tail.
Authors: Flanagan, J.F. / Mi, L.Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT OF THE PROTEIN IS UNKNOWN.
Remark 999SEQUENCE Tyrosine at position 20 is a synthetic modification and does not exist in the histone H3

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 1
B: Chromodomain-helicase-DNA-binding protein 1
C: Chromodomain-helicase-DNA-binding protein 1
D: Histone H3


Theoretical massNumber of molelcules
Total (without water)60,2704
Polymers60,2704
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.268, 55.167, 100.507
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22146.762 Da / Num. of mol.: 2 / Fragment: residues 268-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646
#2: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1


Mass: 13694.292 Da / Num. of mol.: 1 / Fragment: residues 268-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646
#3: Protein/peptide Histone H3


Mass: 2282.668 Da / Num. of mol.: 1 / Fragment: residues 1-19 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans).
References: UniProt: P68431
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 283 K / pH: 8
Details: 4% PEG3350, 0.05M HEPES pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21039 / % possible obs: 93.6 % / Redundancy: 3.5 % / Rsym value: 0.052 / Net I/σ(I): 23.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.221 / % possible all: 65.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B2T WITHOUT CHAIN D

2b2t


Resolution: 2.4→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 238 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1420 6.3 %RANDOM
Rwork0.215 ---
obs0.215 20757 92.5 %-
all-21039 --
Solvent computationBsol: 37.54 Å2
Displacement parametersBiso mean: 43.36 Å2
Baniso -1Baniso -2Baniso -3
1-11.22 Å20 Å21.535 Å2
2---9.125 Å20 Å2
3----2.095 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 0 301 3888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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