[English] 日本語
Yorodumi
- PDB-1kna: Chromo domain of HP1 complexed with histone H3 tail containing di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kna
TitleChromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
Components
  • HETEROCHROMATIN PROTEIN 1
  • METHYLATED Histone H3
KeywordsSTRUCTURAL PROTEIN / chromo / HP1 / histone / dimethyllysine / methyllysine / H3
Function / homology
Function and homology information


protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / satellite DNA binding / : / positive regulation of DNA methylation-dependent heterochromatin formation / chromocenter / pericentric heterochromatin formation / polytene chromosome / rDNA binding / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / nucleosomal DNA binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / heterochromatin formation / condensed chromosome / methylated histone binding / telomere maintenance / Hsp70 protein binding / euchromatin / nucleosome assembly / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / mitotic cell cycle / chromosome / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3 / Heterochromatin protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJacobs, S.A. / Khorasanizadeh, S.
CitationJournal: Science / Year: 2002
Title: Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail.
Authors: Jacobs, S.A. / Khorasanizadeh, S.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HETEROCHROMATIN PROTEIN 1
P: METHYLATED Histone H3


Theoretical massNumber of molelcules
Total (without water)10,3422
Polymers10,3422
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.792, 76.883, 75.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-146-

HOH

-
Components

#1: Protein HETEROCHROMATIN PROTEIN 1 / / HP1 / NONHISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN


Mass: 8586.468 Da / Num. of mol.: 1 / Fragment: Residues 23-76 / Mutation: K38M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3)pLysS / References: UniProt: P05205
#2: Protein/peptide METHYLATED Histone H3


Mass: 1756.017 Da / Num. of mol.: 1 / Fragment: Residues 1-16 / Mutation: P16Y / Source method: obtained synthetically
Details: Synthetic peptide Corresponding to residues 1-16 of Histone H3. K9 dimethylated. P16Y mutation.
References: UniProt: P02299
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 6.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetails
1ammonium sulfate1reservoir
2MES1reservoirpH6.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 6032 / Num. obs: 6032 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 61.6
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 10.5 / Num. unique all: 842 / Rsym value: 0.279 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.279

-
Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.63 Å / Rfactor Rfree error: 0.026 / Data cutoff high rms absF: 117307.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 654 10.9 %RANDOM
Rwork0.228 ---
all-6008 --
obs-5354 99.8 %-
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.6 Å2-3.48 Å2-2.11 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms499 0 0 86 585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.59
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 116 12.1 %
Rwork0.245 842 -
obs--99.3 %
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.59

+
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