[English] 日本語
Yorodumi
- PDB-7vyw: Crystal structure of the chromodomain of Arabidopsis LHP1 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vyw
TitleCrystal structure of the chromodomain of Arabidopsis LHP1 in complex with methylated histone H3K9 peptide
Components
  • Chromo domain-containing protein LHP1
  • methylated histone H3K9 peptide
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


photoperiodism / vernalization response / shoot system morphogenesis / negative regulation of flower development / multidimensional cell growth / photoperiodism, flowering / GTP cyclohydrolase II activity / flower development / negative regulation of gene expression, epigenetic / heterochromatin ...photoperiodism / vernalization response / shoot system morphogenesis / negative regulation of flower development / multidimensional cell growth / photoperiodism, flowering / GTP cyclohydrolase II activity / flower development / negative regulation of gene expression, epigenetic / heterochromatin / heterochromatin formation / methylated histone binding / chloroplast / euchromatin / chromatin organization / sequence-specific DNA binding / cell differentiation / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / identical protein binding / nucleus
Similarity search - Function
Chromo domain-containing protein LHP1 / 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 domain-containing protein LHP1 / 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 / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromo domain-containing protein LHP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Zhang, M. / Min, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500615 China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain.
Authors: Liu, Y. / Yang, X. / Zhou, M. / Yang, Y. / Li, F. / Yan, X. / Zhang, M. / Wei, Z. / Qin, S. / Min, J.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 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: Chromo domain-containing protein LHP1
B: methylated histone H3K9 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5805
Polymers7,2912
Non-polymers2883
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-30 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.088, 28.547, 70.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chromo domain-containing protein LHP1


Mass: 6574.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q946J8
#2: Protein/peptide methylated histone H3K9 peptide


Mass: 716.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes, pH 7.5, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→35.26 Å / Num. obs: 6673 / % possible obs: 90.29 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.57 Å2 / CC1/2: 0.982 / Net I/σ(I): 23.2
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 294 / CC1/2: 0.968

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3L

1q3l


Resolution: 1.6→35.26 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 335 5.02 %
Rwork0.182 6338 -
obs0.1843 6673 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.2 Å2 / Biso mean: 9.8733 Å2 / Biso min: 1.8 Å2
Refinement stepCycle: final / Resolution: 1.6→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms437 0 15 59 511
Biso mean--22.06 19.04 -
Num. residues----53
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.24551670.18113044321189
2.02-35.260.22421680.18243294346292

+
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://pdbjlvh1.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