[English] 日本語
Yorodumi
- PDB-8ily: Crystal structure of the RRM domain of human SETD1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ily
TitleCrystal structure of the RRM domain of human SETD1A
ComponentsSET domain containing 1A, histone lysine methyltransferase
KeywordsSTRUCTURAL PROTEIN / SETD1A / RRM
Function / homology
Function and homology information


: / histone H3K4 methyltransferase activity / RNA binding
Similarity search - Function
Set1A, RNA recognition motif / Histone-lysine N-methyltransferase Set1-like / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
SET domain containing 1A, histone lysine methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
Authors: Bao, S. / Xu, C.
History
DepositionMar 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SET domain containing 1A, histone lysine methyltransferase
B: SET domain containing 1A, histone lysine methyltransferase


Theoretical massNumber of molelcules
Total (without water)25,2832
Polymers25,2832
Non-polymers00
Water4,450247
1
A: SET domain containing 1A, histone lysine methyltransferase


Theoretical massNumber of molelcules
Total (without water)12,6421
Polymers12,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SET domain containing 1A, histone lysine methyltransferase


Theoretical massNumber of molelcules
Total (without water)12,6421
Polymers12,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.542, 31.675, 65.579
Angle α, β, γ (deg.)90.000, 94.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein SET domain containing 1A, histone lysine methyltransferase


Mass: 12641.687 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD1A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A804HLA6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.66 Å3/Da / Density % sol: 26.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 4M Sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→40.41 Å / Num. obs: 18532 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05272 / Net I/σ(I): 21.32
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 18532 / CC1/2: 0.989

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT1.20.1_4487data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.2 Å / SU ML: 0.1768 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.3744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 855 4.61 %
Rwork0.1816 17677 -
obs0.184 18532 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 0 247 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691808
X-RAY DIFFRACTIONf_angle_d0.92122436
X-RAY DIFFRACTIONf_chiral_restr0.0647279
X-RAY DIFFRACTIONf_plane_restr0.0092310
X-RAY DIFFRACTIONf_dihedral_angle_d5.3441244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.25451420.20032847X-RAY DIFFRACTION98.06
1.81-1.950.27431470.1882941X-RAY DIFFRACTION99.9
1.95-2.140.22061460.1772951X-RAY DIFFRACTION99.84
2.14-2.450.26791550.19162926X-RAY DIFFRACTION99.87
2.45-3.090.2421130.19232977X-RAY DIFFRACTION99.87
3.09-33.20.20761520.16553035X-RAY DIFFRACTION99.56

+
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