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- PDB-1m18: LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA -

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Basic information

Entry
Database: PDB / ID: 1m18
TitleLIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
Components
  • Histone H2A.1
  • Histone H2B.1
  • Histone H3.2
  • Histone H4
  • Palindromic 146 Base Pair DNA Fragment
KeywordsSTRUCTURAL PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / PYRROLE-IMIDAZOLE POLYAMIDE / DNA REGOGNITION / CHROMATIN REMODELING / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


chromatin organization => GO:0006325 / chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...chromatin organization => GO:0006325 / chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein domain specific binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1SZ / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H3.3C / Histone H4 / Histone H2A type 1 / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSuto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands
Authors: Suto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 17, 2013Group: Database references / Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
I: Palindromic 146 Base Pair DNA Fragment
J: Palindromic 146 Base Pair DNA Fragment
A: Histone H3.2
B: Histone H4
C: Histone H2A.1
D: Histone H2B.1
E: Histone H3.2
F: Histone H4
G: Histone H2A.1
H: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,94623
Polymers198,89710
Non-polymers3,04913
Water9,242513
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.839, 109.628, 183.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 2 molecules IJ

#1: DNA chain Palindromic 146 Base Pair DNA Fragment


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.2


Mass: 15320.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02302
#3: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02304, UniProt: P62799*PLUS
#4: Protein Histone H2A.1


Mass: 13962.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein Histone H2B.1


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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Non-polymers , 3 types, 526 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-1SZ / N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene-butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole-2-carboxamide / PYRROLE-IMIDAZOLE POLYAMIDE


Mass: 1222.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C58H71N21O10
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND SEQUENCE ...AUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND SEQUENCE DATABASE REFERENCE SWISSPROT ENTRY P02302. SER WAS CRYSTALLIZED AT POSITION 486,686 FOR CHAINS A,E. AUTHOR INFORMS GLY-ARG MISMATCH AT RESIDUE 899,1099 (CHAINS C,G) AND SER-THR MISMATCH AT RESIDUE 1229,1429 (CHAINS D,H) ARE VARIANTS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140-45 mM1reservoirMnCl2
235-38.8 mM1reservoirKCl
320 mMpotassium cacodylate1droppH6.0
44 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.45→60 Å / Num. all: 79809 / Num. obs: 77428 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.2
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.3 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 60 Å / Num. obs: 79809 / % possible obs: 98.4 %
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOI

1aoi


Resolution: 2.45→60 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2351 -random
Rwork0.222 ---
all-79809 --
obs-77428 97.1 %-
Refinement stepCycle: LAST / Resolution: 2.45→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 5980 154 513 12676
Refinement
*PLUS
Lowest resolution: 60 Å / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.12

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