[English] 日本語
Yorodumi
- PDB-4es0: X-ray structure of WDR5-SETd1b Win motif peptide binary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4es0
TitleX-ray structure of WDR5-SETd1b Win motif peptide binary complex
Components
  • Histone-lysine N-methyltransferase SETD1B
  • WD repeat-containing protein 5
KeywordsTranscription/Transferase / WD40 / Win motif / beta propeller / 3-10 helix / lysine methyltransferase / SETd1b / RbBP5 / MLL1 / Ash2L / core complex / Histone / Transcription-Transferase complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone H3 methyltransferase activity / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / chromosome / Neddylation / methylation / HATs acetylate histones / histone binding / regulation of cell cycle / nuclear speck / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Set1B, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / 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 ...Set1B, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / 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 superfamily / SET domain / SET domain profile. / SET domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone-lysine N-methyltransferase SETD1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.817 Å
AuthorsDharmarajan, V. / Lee, J.-H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for WDR5 interaction (Win) motif recognition in human SET1 family histone methyltransferases.
Authors: Dharmarajan, V. / Lee, J.H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
History
DepositionApr 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 5
C: Histone-lysine N-methyltransferase SETD1B


Theoretical massNumber of molelcules
Total (without water)35,8632
Polymers35,8632
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.254, 98.272, 79.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34303.914 Da / Num. of mol.: 1 / Fragment: UNP residues 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIG3, WDR5 / Plasmid: pHIS paralell / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P61964
#2: Protein/peptide Histone-lysine N-methyltransferase SETD1B / Lysine N-methyltransferase 2G / SET domain-containing protein 1B / hSET1B


Mass: 1558.671 Da / Num. of mol.: 1 / Fragment: UNP residues 1698-1711 / Source method: obtained synthetically / Details: SETd1b Win motif peptide (1698-1711) / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UPS6, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 7.6
Details: PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionRedundancy: 13.2 % / Av σ(I) over netI: 60.92 / Number: 365152 / Rmerge(I) obs: 0.13 / Χ2: 8.13 / D res high: 1.81 Å / D res low: 50 Å / Num. obs: 27686 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.9509710.0879.0612.5
3.093.996.210.1028.48712.3
2.73.0999.910.1359.43413.7
2.462.710010.1669.45213.8
2.282.4610010.199.41613.7
2.152.2810010.2139.0713.7
2.042.1510010.2388.29413.7
1.952.0410010.2786.83513.7
1.871.9510010.325.70413.4
1.811.8789.810.3774.53411.2
ReflectionResolution: 1.81→50 Å / Num. obs: 27686 / % possible obs: 98.3 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.13 / Χ2: 8.132 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.81-1.8711.20.37724794.534189.8
1.87-1.9513.40.3228035.7041100
1.95-2.0413.70.27827666.8351100
2.04-2.1513.70.23827778.2941100
2.15-2.2813.70.21327949.071100
2.28-2.4613.70.1928029.4161100
2.46-2.713.80.16628039.4521100
2.7-3.0913.70.13528319.434199.9
3.09-3.912.30.10227568.487196.2
3.9-5012.50.08728759.06197

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.817→41.852 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.7891 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1370 5.03 %
Rwork0.2144 --
obs0.2158 27254 97.02 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.389 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 60.12 Å2 / Biso mean: 24.3772 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--8.939 Å20 Å2-0 Å2
2--20.1173 Å20 Å2
3----11.1784 Å2
Refinement stepCycle: LAST / Resolution: 1.817→41.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 106 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072457
X-RAY DIFFRACTIONf_angle_d1.1543330
X-RAY DIFFRACTIONf_chiral_restr0.077375
X-RAY DIFFRACTIONf_plane_restr0.005414
X-RAY DIFFRACTIONf_dihedral_angle_d12.782870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.817-1.88220.37491410.29432361250290
1.8822-1.95760.33721510.27322575272698
1.9576-2.04670.30661290.23722569269898
2.0467-2.15460.26611340.20842638277299
2.1546-2.28960.24751460.2082583272999
2.2896-2.46630.26771360.20492601273798
2.4663-2.71450.28611370.21352608274598
2.7145-3.10720.21181350.21362643277898
3.1072-3.91430.20261300.19472593272395
3.9143-41.8520.21041310.21122713284497

+
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