[English] 日本語
Yorodumi
- PDB-3kxb: Structural characterization of H3K56Q nucleosomes and nucleosomal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kxb
TitleStructural characterization of H3K56Q nucleosomes and nucleosomal arrays
Components
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
KeywordsTranscription/DNA / Nucleosome / Transcription / Transcription-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
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsClark, N.J. / Lilyestrom, W.G.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.
Authors: Watanabe, S. / Resch, M. / Lilyestrom, W. / Clark, N. / Hansen, J.C. / Peterson, C. / Luger, K.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
J: PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA


Theoretical massNumber of molelcules
Total (without water)198,25010
Polymers198,25010
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52780 Å2
ΔGint-363 kcal/mol
Surface area73830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.517, 105.670, 181.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsA single nucleosome is in the asymmetric unit. One nucleosome is composed of 2 chains each of the four histones (H2A, H2B, H3 and H4) in an octamer as well as 146 base pairs of double stranded DNA. No symmetry operations are required to build the biological unit.

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15303.863 Da / Num. of mol.: 2 / Mutation: K57E, G103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P84233
#2: 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) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62799
#3: Protein Histone H2A /


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2 / Mutation: S33T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P02281

-
DNA chain / Non-polymers , 2 types, 117 molecules IJ

#5: DNA chain PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, ...Details: Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 17, 2007 / Details: Rigaku Varimax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 35254 / Num. obs: 35254 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.3 % / Biso Wilson estimate: 79.7 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.53
Reflection shellHighest resolution: 3.2 Å / % possible all: 78

-
Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1AOI

1aoi


Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 2738 -Random
Rwork0.2835 ---
all0.378 35254 --
obs0.378 27493 78 %-
Displacement parametersBiso mean: 79.7 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5773 5980 0 115 11868

+
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