[English] 日本語
Yorodumi
- PDB-2nzd: Nucleosome core particle containing 145 bp of DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nzd
TitleNucleosome core particle containing 145 bp of DNA
Components
  • (DNA (145-MER)) x 2
  • Histone H2B
  • Histone H3
  • Histone H4
  • histone H2A
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone / DNA stretching / DNA kinking / double-helix / 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
: / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsOng, M.S. / Richmond, T.J. / Davey, C.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: DNA stretching and extreme kinking in the nucleosome core
Authors: Ong, M.S. / Richmond, T.J. / Davey, C.A.
History
DepositionNov 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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_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.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: DNA (145-MER)
J: DNA (145-MER)
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)196,80721
Polymers196,20310
Non-polymers60411
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.617, 109.856, 181.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA (145-MER)


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Protein , 4 types, 8 molecules AEBFCGDH

#3: 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) / Production host: Escherichia coli (E. coli) / References: GenBank: 288992, UniProt: P84233*PLUS
#4: 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) / References: UniProt: P62799
#5: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: Protein Histone H2B / / H2B1.1


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

-
Non-polymers , 2 types, 133 molecules

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


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MnCl211
2KCl11
3K-Cacodylate11
4HOH11
5MnCl212
6KCl12
7K-Cacodylate12
8HOH12

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 5, 2006 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.65→50.7 Å / Num. all: 61751 / Num. obs: 56193 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.9
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / Num. measured all: 27467 / Num. unique all: 5579 / Rsym value: 0.48 / % possible all: 63.9

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KX3

1kx3


Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.836 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1136 2 %RANDOM
Rwork0.233 ---
all0.234 61932 --
obs0.234 56123 90.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---1.09 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 5939 11 122 12158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112821
X-RAY DIFFRACTIONr_angle_refined_deg1.452.54318556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50921.338269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.427151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371584
X-RAY DIFFRACTIONr_chiral_restr0.0740.22113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027545
X-RAY DIFFRACTIONr_nbd_refined0.2060.24850
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2396
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.25
X-RAY DIFFRACTIONr_mcbond_it0.7271.53872
X-RAY DIFFRACTIONr_mcangle_it1.29226110
X-RAY DIFFRACTIONr_scbond_it1.234312076
X-RAY DIFFRACTIONr_scangle_it2.2024.512446
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 59 -
Rwork0.302 2573 -
obs-2632 58.46 %

+
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