[English] 日本語
Yorodumi
- PDB-1s32: Molecular Recognition of the Nucleosomal 'Supergroove' -

+
Open data


ID or keywords:

Loading...

-
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 / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / 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 domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2
#10: Chemical ChemComp-BAL / BETA-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)


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


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


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more