[English] 日本語
Yorodumi
- PDB-2l7p: ASHH2 a CW domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l7p
TitleASHH2 a CW domain
ComponentsHistone-lysine N-methyltransferase ASHH2
KeywordsTRANSFERASE / CW-domain
Function / homology
Function and homology information


carotenoid metabolic process / response to nitrate starvation / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development / regulation of programmed cell death ...carotenoid metabolic process / response to nitrate starvation / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development / regulation of programmed cell death / SUMO binding / histone H3K4 methyltransferase activity / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / epigenetic regulation of gene expression / methylation / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SETD2/Set2, SET domain / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains ...Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SETD2/Set2, SET domain / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
Histone-lysine N-methyltransferase ASHH2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKristiansen, P. / Hoppmann, V. / Thorstensen, T. / Aalen, R.B. / Aasland, R. / Finne, K. / Veiseth, S.
CitationJournal: Embo J. / Year: 2011
Title: The CW domain, a new histone recognition module in chromatin proteins.
Authors: Hoppmann, V. / Thorstensen, T. / Kristiansen, P.E. / Veiseth, S.V. / Rahman, M.A. / Finne, K. / Aalen, R.B. / Aasland, R.
History
DepositionDec 16, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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
A: Histone-lysine N-methyltransferase ASHH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2792
Polymers11,2131
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Histone-lysine N-methyltransferase ASHH2 / ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein ...ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein EARLY FLOWERING IN SHORT DAYS / Protein SET DOMAIN GROUP 8


Mass: 11213.218 Da / Num. of mol.: 1 / Fragment: CW-type zinc finger residues 849-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ASHH2, EFS, SDG8, SET8, At1g77300, T14N5.15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2LAE1, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D HNHA
11213D HN(COCA)CB
11313D HBHANH
11413D HN(CA)CO
11513D HN(CO)CA
11613D 1H-15N NOESY
11713D 1H-13C NOESY
11811D 1H proton spectrum water suppresion with exitation sculptin

-
Sample preparation

DetailsContents: 0.8 mM [U-98% 13C; U-98% 15N] protein, 10 uM ZINC ION, 0.2 mM DSS, 1.0 mM DTT, 20 mM potassium phosphate, 50 mM potassium chloride, 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMprotein_1-1[U-98% 13C; U-98% 15N]1
10 uMZINC ION-21
0.2 mMDSS-31
1.0 mMDTT-41
20 mMpotassium phosphate-51
50 mMpotassium chloride-61
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Herrmann, Guntert and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospinforuier transform
CYANA2.1Herrmann, Guntert and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1400 / NOE intraresidue total count: 414 / NOE long range total count: 269 / NOE medium range total count: 296 / NOE sequential total count: 381 / Disulfide bond constraints total count: 28 / Hydrogen bond constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.006 Å / Distance rms dev error: 0.001 Å

+
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