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- PDB-1s32: Molecular Recognition of the Nucleosomal 'Supergroove' -

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Basic information

Entry
Database: PDB / ID: 1s32
TitleMolecular Recognition of the Nucleosomal 'Supergroove'
Components
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • palindromic alpha-satellite 146 bp DNA fragment
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome Core Particle (NCP) / Pyrrole-Imidazole (Py-Im) hairpin polyamide / clamp / nucleosome dynamics / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / 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. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold 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 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / BETA-ALANINE / 3-AMINO-(DIMETHYLPROPYLAMINE) / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID / : / 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID / DNA / DNA (> 10) / DNA (> 100) ...GAMMA-AMINO-BUTANOIC ACID / BETA-ALANINE / 3-AMINO-(DIMETHYLPROPYLAMINE) / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID / : / 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Histone H4 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsEdayathumangalam, R.S. / Weyermann, P. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Molecular Recognition of the Nucleosomal 'Supergroove'
Authors: Edayathumangalam, R.S. / Weyermann, P. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: palindromic alpha-satellite 146 bp DNA fragment
J: palindromic alpha-satellite 146 bp DNA fragment
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,09851
Polymers196,17610
Non-polymers3,92241
Water15,997888
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.352, 109.717, 181.827
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 alpha-satellite 146 bp DNA fragment


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3 /


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A310TTQ1, UniProt: P84233*PLUS
#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) / Gene: LOC121398084 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A8J1LTD2, UniProt: P62799*PLUS
#4: Protein Histone H2A /


Mass: 12941.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#5: Protein Histone H2B /


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A8J0U496, UniProt: P02281*PLUS

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Non-polymers , 9 types, 929 molecules

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


Mass: 54.938 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-IMT / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID


Mass: 141.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7N3O2
#8: Chemical
ChemComp-PYB / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID


Mass: 140.140 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H8N2O2
#9: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#10: Chemical ChemComp-BAL / BETA-ALANINE / Β-Alanine


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#11: Chemical ChemComp-DIB / 3-AMINO-(DIMETHYLPROPYLAMINE) / Dimethylaminopropylamine


Mass: 102.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N2
#12: Chemical ChemComp-OGG / 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE


Mass: 176.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O4
#13: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.99 Å3/Da / Density % sol: 58.56 %
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
Components of the solutions
IDNameCrystal-IDSol-ID
1Manganese chloride11
2potassium chloride11
3potassium cacodylate11
4H2O11
5Manganese chloride12
6potassium chloride12
7H2O12

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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 210 / Detector: CCD / Date: May 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. obs: 124523 / % possible obs: 94.4 % / Redundancy: 4.75 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.99
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.04 / % possible all: 54.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOI

1aoi


Resolution: 2.05→100 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: THE STRUCTURE HAS SOME UNMODELLED POTENTIAL ALTERNATE AMINO ACID SIDE CHAIN CONFORMERS, SOLVENT ENTITIES AND SOME UNACCOUNTED SPURIOUS DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 6050 -Random
Rwork0.2194 ---
all-124523 --
obs-120181 90.7 %-
Refinement stepCycle: LAST / Resolution: 2.05→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 5980 208 888 13279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.099

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