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- PDB-2b2t: Tandem chromodomains of human CHD1 complexed with Histone H3 Tail... -

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Basic information

Entry
Database: PDB / ID: 2b2t
TitleTandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3
Components
  • (Chromodomain-helicase-DNA-binding protein 1) x 2
  • Histone H3 tail
KeywordsPEPTIDE BINDING PROTEIN / CHD / Chromodomain / three stranded antiparallel Beta sheet / alpha helix linker / histone H3 / trimethyllysine / phosphothreonine
Function / homology
Function and homology information


nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / 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 / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / 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 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / 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 / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / 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 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...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 / 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 / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 / MAD / Resolution: 2.45 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
Remark 999SEQUENCE Selenomethionine at position 1 in chains A, B, C is a modified methionine residue and a ...SEQUENCE Selenomethionine at position 1 in chains A, B, C is a modified methionine residue and a cloning artifact. Selenomethionine at position 178 is a modified residue and a result of C436M mutation in chains A and B. Tyrosine at position 20 is a synthetic modification and does not exist in histone H3
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.

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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: Chromodomain-helicase-DNA-binding protein 1
C: Chromodomain-helicase-DNA-binding protein 1
D: Histone H3 tail


Theoretical massNumber of molelcules
Total (without water)60,9224
Polymers60,9224
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.986, 54.686, 100.989
Angle α, β, γ (deg.)90.00, 112.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

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Components

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


Mass: 22362.396 Da / Num. of mol.: 2 / Fragment: residues 268-443 / Mutation: C436M
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: 13834.978 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 tail


Mass: 2362.648 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.: 258 / 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: 3

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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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926, 0.97939, 0.97240
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL CRYSTAL DOUBLE CRYSTALMADMx-ray1
2Mx-ray1
3Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979391
30.97241
Reflection

D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
3.81140570.081.0772.898.5
3.72217310.0711.0482.497.3
3.83175110.0681.0582.698.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035098.710.0422.0113.7
4.796.0399.210.0481.2233.8
4.184.7999.210.0561.3813.8
3.84.1898.810.0721.2273.8
3.533.898.910.0961.113.8
3.323.5398.610.1320.9443.8
3.153.3298.710.1860.8153.9
3.023.1598.610.2670.7053.9
2.93.0298.510.3890.6523.8
2.82.996.210.5250.6123.4
5.175098.920.0482.5053.7
4.15.1799.120.0471.5483.8
3.584.198.820.0541.193.8
3.263.589920.0731.0343.8
3.023.2698.620.0990.8583.9
2.853.0298.620.1530.6793.9
2.72.8598.420.2260.6223.8
2.592.798.220.3080.5973.7
2.492.5995.720.3480.5683.3
2.42.4987.720.4260.5652.9
5.65098.730.0422.3463.7
4.455.699.330.0431.4493.8
3.884.4598.830.0481.263.8
3.533.8898.830.0631.1513.8
3.283.5398.830.0840.9933.8
3.083.2898.730.1130.7913.9
2.933.0898.630.1730.6983.9
2.82.9398.530.2610.6113.8
2.692.897.930.3580.5863.7
2.62.6995.730.4470.5753.3
ReflectionResolution: 2.4→40.2 Å / Num. obs: 21731 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rsym value: 0.071 / Net I/σ(I): 15.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.426 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 41 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1337 6.3 %RANDOM
Rwork0.218 ---
obs0.218 19575 93 %-
all-21731 --
Solvent computationBsol: 43.21 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 47.86 Å2
Baniso -1Baniso -2Baniso -3
1-6.794 Å20 Å2-3.542 Å2
2---3.654 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 0 258 3868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.88
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
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 20 /
Num. reflection% reflection
Rwork1964 -
obs-87.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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