[English] 日本語
Yorodumi
- PDB-3uta: Crystal Structure of Nucleosome Core Particle Assembled with an A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uta
TitleCrystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2)
Components
  • (145-mer DNA) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome core particle / NCP / alpha satellite DNA / 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 H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of 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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The mechanics behind DNA sequence-dependent properties of the nucleosome
Authors: Chua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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

-
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: 145-mer DNA
J: 145-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,34731
Polymers198,27110
Non-polymers1,07621
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60000 Å2
ΔGint-492 kcal/mol
Surface area72510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.510, 109.910, 182.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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: hist1h2aj, LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain 145-mer DNA


Mass: 44746.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#6: DNA chain 145-mer DNA


Mass: 44737.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct

-
Non-polymers , 3 types, 130 molecules

#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsUNINTENTIONAL MUTATIONS OR VARIATIONS IN GENOMIC SOURCES.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Mosaicity: 0.25 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.067→94.13 Å / Num. all: 99095 / Num. obs: 99095 / % possible obs: 75.7 % / Redundancy: 4.2 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Rsym value: 0.062 / Net I/av σ(I): 3.153 / Net I/σ(I): 12.1 / Num. measured all: 413096
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.07-2.181.50.6010.4521.4441228720.4110.6010.4521.415.4
2.18-2.311.90.3560.2422.71536082460.2330.3560.2422.446.7
2.31-2.472.30.2320.164.328158121210.140.2320.163.973
2.47-2.673.10.1580.1165.845242144200.0840.1580.1166.292.5
2.67-2.925.20.1170.0966.875505144970.050.1170.09610.999.8
2.92-3.275.90.090.0757.977222131770.0380.090.07515.6100
3.27-3.775.60.0720.069.865408116880.0310.0720.0619.6100
3.77-4.624.70.0650.05310.64702799100.030.0650.05320.299.8
4.62-6.544.70.0630.05110.53598877250.0290.0630.05120.499.6
6.54-106.514.20.0790.0634.61877444390.0370.0790.06320.699.3

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→94.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.3025 / WRfactor Rwork: 0.2758 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7802 / SU B: 5.617 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2754 / SU Rfree: 0.2151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 2009 2 %RANDOM
Rwork0.2405 ---
obs0.2411 99013 75.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 156.92 Å2 / Biso mean: 67.4383 Å2 / Biso min: 17.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.07→94.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 5939 21 109 12155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112821
X-RAY DIFFRACTIONr_angle_refined_deg1.4182.54318556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.895757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5721.338269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.446151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6911584
X-RAY DIFFRACTIONr_chiral_restr0.0690.22113
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027545
X-RAY DIFFRACTIONr_mcbond_it0.7851.53797
X-RAY DIFFRACTIONr_mcangle_it1.52126110
X-RAY DIFFRACTIONr_scbond_it1.51639024
X-RAY DIFFRACTIONr_scangle_it2.4424.512446
LS refinement shellResolution: 2.067→2.121 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 13 -
Rwork0.3 709 -
all-722 -
obs--7.51 %

+
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