[English] 日本語
Yorodumi
- PDB-1pfb: Structural Basis for specific binding of polycomb chromodomain to... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pfb
TitleStructural Basis for specific binding of polycomb chromodomain to histone H3 methylated at K27
Components
  • Histone H3, embryonic
  • Polycomb proteinPolycomb-group proteins
KeywordsPEPTIDE BINDING PROTEIN / chromatin / histone methylation / polycomb / chromodomain
Function / homology
Function and homology information


negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development ...negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development / PRC1 complex / polytene chromosome / anterior/posterior axis specification / neuron remodeling / heterochromatin formation / methylated histone binding / neurogenesis / wound healing / nucleosome / sequence-specific DNA binding / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
CBX family C-terminal motif / CBX family C-terminal motif / 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 ...CBX family C-terminal motif / CBX family C-terminal motif / 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
ACETIC ACID / BETA-MERCAPTOETHANOL / Histone H3, embryonic / Polycomb group protein Pc
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMin, J.R. / Zhang, Y. / Xu, R.-M.
CitationJournal: Genes Dev. / Year: 2003
Title: Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27.
Authors: Min, J.R. / Zhang, Y. / Xu, R.-M.
History
DepositionMay 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polycomb protein
B: Histone H3, embryonic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1746
Polymers7,9652
Non-polymers2094
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area4880 Å2
MethodPISA
2
A: Polycomb protein
B: Histone H3, embryonic
hetero molecules

A: Polycomb protein
B: Histone H3, embryonic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,34912
Polymers15,9304
Non-polymers4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area4300 Å2
ΔGint-36 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.429, 77.033, 77.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-204-

CL

31A-205-

HOH

41A-332-

HOH

51A-339-

HOH

61A-340-

HOH

71A-341-

HOH

81B-2-

HOH

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Polycomb protein / Polycomb-group proteins


Mass: 6806.826 Da / Num. of mol.: 1 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PC OR CG7618 / Production host: Escherichia coli (E. coli) / References: UniProt: P26017
#2: Protein/peptide Histone H3, embryonic /


Mass: 1158.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is naturally found in Strongylocentrotus purpuratus.
References: UniProt: P06352

-
Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8000, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
25 %Tris1droppH8.0
3200 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
6100 mMsodium cacodylate1reservoirpH6.5
70.2 Mammonium sulfate1reservoir
830 %PEG80001reservoir
910 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 19520 / Num. obs: 17050 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 42.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 85538 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 42.3 % / Num. unique obs: 811 / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.1

-
Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→27.28 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 1701 random
Rwork0.197 --
all-17050 -
obs-17050 -
Refinement stepCycle: LAST / Resolution: 1.4→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms559 0 6 151 716
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.29
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg24.12
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.7
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.46 Å / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.298

+
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