[English] 日本語
Yorodumi
- PDB-7de9: crystal structure of Arabidopsis RDM15 tudor domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7de9
Titlecrystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide
Components
  • Histone H3.2
  • Transcriptional regulator
KeywordsGENE REGULATION / tudor domain / histone / epigenetics / DNA methylation
Function / homology
Function and homology information


microsporogenesis / chromocenter / plastid / mitotic sister chromatid cohesion / structural constituent of chromatin / nucleosome / protein heterodimerization activity / cell division / DNA repair / chromatin ...microsporogenesis / chromocenter / plastid / mitotic sister chromatid cohesion / structural constituent of chromatin / nucleosome / protein heterodimerization activity / cell division / DNA repair / chromatin / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Sister chromatid cohesion protein Pds5 / 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 / Armadillo-type fold
Similarity search - Domain/homology
Histone H3.1 / Transcriptional regulator
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.711 Å
AuthorsSong, Z. / Du, J.
CitationJournal: Nat Commun / Year: 2021
Title: A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation.
Authors: Niu, Q. / Song, Z. / Tang, K. / Chen, L. / Wang, L. / Ban, T. / Guo, Z. / Kim, C. / Zhang, H. / Duan, C.G. / Zhang, H. / Zhu, J.K. / Du, J. / Lang, Z.
History
DepositionNov 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator
P: Histone H3.2


Theoretical massNumber of molelcules
Total (without water)9,1692
Polymers9,1692
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-3 kcal/mol
Surface area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.579, 36.963, 46.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Transcriptional regulator


Mass: 7590.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g31880, F11C18.80, F11C18_80 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GUP3
#2: Protein/peptide Histone H3.2 / Histone H3.1


Mass: 1578.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.34 Å3/Da / Density % sol: 8.51 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, and 20% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 5630 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.036 / Rrim(I) all: 0.106 / Χ2: 1.245 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7690.55450.8410.1820.5330.61299.8
1.76-1.838.80.4025370.9330.1460.4290.696100
1.83-1.918.60.2935610.940.1090.3140.80299.8
1.91-2.028.10.2485490.950.0940.2661.00799.6
2.02-2.149.30.1995480.9670.0720.2131.157100
2.14-2.319.10.1585560.9840.0560.1681.32299.8
2.31-2.548.90.145590.9820.050.151.404100
2.54-2.918.10.1135650.9890.0430.1211.61899.8
2.91-3.669.10.0875810.9930.030.0921.857100
3.66-508.10.0696290.9920.0260.0741.88899.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.711→28.978 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 464 4.58 %
Rwork0.1834 9672 -
obs0.1843 5595 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.1 Å2 / Biso mean: 32.7157 Å2 / Biso min: 17.85 Å2
Refinement stepCycle: final / Resolution: 1.711→28.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 0 25 542
Biso mean---37.86 -
Num. residues----63
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005529
X-RAY DIFFRACTIONf_angle_d0.954712
X-RAY DIFFRACTIONf_chiral_restr0.03473
X-RAY DIFFRACTIONf_plane_restr0.00487
X-RAY DIFFRACTIONf_dihedral_angle_d16.912195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7112-1.95880.28641470.2187312796
1.9588-2.46760.23121680.20043265100
2.4676-280.17251490.17033280100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.39682.1109-1.87955.9165-2.86863.59930.08120.16490.2116-0.0040.05670.3852-0.3263-0.0885-0.11840.16920.0158-0.02990.1486-0.02770.16468.481218.907419.4705
25.48851.4475-4.05393.4162-0.75718.46560.1441-0.0317-0.2091-0.2587-0.22670.0117-0.42740.31950.09520.18130.0225-0.02230.12780.03420.18612.899920.827719.4693
34.43840.2359-0.62863.5630.15622.11630.0156-0.115-0.12230.015-0.1281-0.21220.10520.23520.090.1629-0.0186-0.0060.17760.01920.196316.633317.5718.3357
42.3213-2.4505-3.80915.58471.57038.2832-0.00940.69620.06080.4023-0.19410.6154-0.3736-0.9269-0.1170.34890.0389-0.0330.3935-0.0110.37696.758516.698214.0415
53.62190.2803-0.33519.28651.52635.79580.0154-0.4586-0.35420.7519-0.17050.0680.5168-0.03860.03250.2316-0.01070.00920.24810.08720.309610.88318.644928.1637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 602 through 620 )A602 - 620
2X-RAY DIFFRACTION2chain 'A' and (resid 621 through 631 )A621 - 631
3X-RAY DIFFRACTION3chain 'A' and (resid 632 through 649 )A632 - 649
4X-RAY DIFFRACTION4chain 'A' and (resid 650 through 658 )A650 - 658
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 5 )P1 - 5

+
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