[English] 日本語
Yorodumi
- PDB-4rt4: Crystal structure of Dpy30 complexed with Bre2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rt4
TitleCrystal structure of Dpy30 complexed with Bre2
Components
  • Peptide from COMPASS component BRE2
  • Protein dpy-30 homolog
KeywordsPROTEIN BINDING / X-type helix / H3K4 methylation
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / subtelomeric heterochromatin formation / transcription initiation-coupled chromatin remodeling ...Formation of WDR5-containing histone-modifying complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / subtelomeric heterochromatin formation / transcription initiation-coupled chromatin remodeling / telomere maintenance / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / trans-Golgi network / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / chromosome, telomeric region / transcription cis-regulatory region binding / Golgi apparatus / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / cAMP-dependent Protein Kinase, Chain A / Histone methyltransferase complex subunit ASH2 / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. ...: / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / cAMP-dependent Protein Kinase, Chain A / Histone methyltransferase complex subunit ASH2 / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
COMPASS component BRE2 / Protein dpy-30 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsZhang, H.M. / Li, M. / Chang, W.R.
CitationJournal: Protein Cell / Year: 2015
Title: Structural implications of Dpy30 oligomerization for MLL/SET1 COMPASS H3K4 trimethylation
Authors: Zhang, H. / Li, M. / Gao, Y. / Jia, C. / Pan, X. / Cao, P. / Zhao, X. / Zhang, J. / Chang, W.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Dec 25, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
C: Protein dpy-30 homolog
D: Protein dpy-30 homolog
E: Peptide from COMPASS component BRE2


Theoretical massNumber of molelcules
Total (without water)33,8895
Polymers33,8895
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.229, 75.229, 105.758
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Protein dpy-30 homolog / Dpy-30-like protein / Dpy-30L


Mass: 7581.706 Da / Num. of mol.: 4 / Fragment: C terminal domain, UNP residues 41-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPY30 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C005
#2: Protein/peptide Peptide from COMPASS component BRE2 / / Brefeldin-A sensitivity protein 2 / Complex proteins associated with SET1 protein BRE2 / Set1C component BRE2


Mass: 3561.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P43132
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.1M Tris-HCl, pH 8.5, 2.0M NH4H2PO4, EVAPORATION, temperature 291K
PH range: PH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. all: 23040 / Num. obs: 23016 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.051 / Net I/σ(I): 35.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.0511.30.3962.40.9231100
2.05-2.111.40.813.30.671100
2.1-2.1511.40.694.40.521100
2.15-2.2211.40.396.90.31100
2.22-2.2911.40.338.50.271100
2.29-2.3711.40.279.90.221100
2.37-2.4711.40.213.90.171100
2.47-2.5811.40.1923.50.151100
2.58-2.7111.40.1218.30.11100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G36

3g36


Resolution: 1.997→35.44 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1179 5.13 %
Rwork0.18 --
obs0.1822 22964 99.77 %
all-23033 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 0 173 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071970
X-RAY DIFFRACTIONf_angle_d1.0432698
X-RAY DIFFRACTIONf_dihedral_angle_d15.728773
X-RAY DIFFRACTIONf_chiral_restr0.046317
X-RAY DIFFRACTIONf_plane_restr0.006354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9975-2.08840.26621560.24172714X-RAY DIFFRACTION100
2.0884-2.19850.2411200.20672723X-RAY DIFFRACTION100
2.1985-2.33620.21911590.20382691X-RAY DIFFRACTION100
2.3362-2.51650.23481680.18892710X-RAY DIFFRACTION100
2.5165-2.76970.2081470.18892739X-RAY DIFFRACTION100
2.7697-3.17030.22171520.17942717X-RAY DIFFRACTION100
3.1703-3.99330.18891390.16792735X-RAY DIFFRACTION100
3.9933-35.44530.24911380.17042756X-RAY DIFFRACTION99
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)
12.17582.7242-0.49628.72041.83028.82840.0110.1959-0.8636-0.3028-0.2629-0.78970.7040.10470.16420.37740.03670.09430.2575-0.00850.405412.7061-52.231814.5507
22.88490.29930.53812.3984-0.65863.0088-0.0034-0.31980.4950.2636-0.1847-0.2645-0.160.06690.16870.2605-0.0388-0.02290.2404-0.02190.291211.5845-33.459121.0561
38.1556-1.9814-1.472.75340.10537.2456-0.2534-0.23721.08650.4860.06210.2612-0.3238-0.63650.10820.30490.0544-0.00750.3256-0.08730.3946-1.5726-28.688815.3795
43.0583-1.7387-0.07833.6209-0.96331.7686-0.09810.41850.0397-0.2837-0.1694-0.5090.31060.1170.20740.22650.00610.03570.3018-0.00060.304212.4002-42.50138.5783
54.2001-0.56651.46364.5789-2.45225.564-0.14770.54330.1512-0.08010.15160.0033-0.27340.0483-0.00890.2286-0.03760.02890.31380.0340.338715.6489-34.11548.9556
66.01550.1474-0.32093.77130.26054.1037-0.0321-0.19370.01230.1414-0.1280.2044-0.2599-0.21220.16330.31040.0274-0.04070.2373-0.03010.1537-3.2798-47.797135.7542
73.634-1.2415-2.19563.26980.71476.2107-0.1393-0.0485-0.22130.17390.13280.36940.356-0.3578-0.01990.3141-0.00490.00910.25010.0050.285-2.297-56.897439.2979
86.72120.68-0.11013.87080.73194.1898-0.20260.1493-0.02-0.15920.0374-0.1939-0.29210.24050.0960.279-0.0115-0.04510.18770.04360.16093.2622-47.769429.319
94.43121.8953-3.02333.3973-1.08166.3205-0.26030.0739-0.4874-0.213-0.0995-0.38180.35330.17310.25130.31310.00590.01280.23710.00160.25922.243-56.892125.8221
105.03480.05330.15943.1357-2.28923.63320.20880.5303-0.20150.3242-0.49970.6869-0.1601-1.38320.14690.5146-0.0899-0.11740.55660.25910.69380.2947-43.1615.6554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 96 )
3X-RAY DIFFRACTION3chain 'B' and (resid 47 through 61 )
4X-RAY DIFFRACTION4chain 'B' and (resid 62 through 79 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 96 )
6X-RAY DIFFRACTION6chain 'C' and (resid 47 through 79 )
7X-RAY DIFFRACTION7chain 'C' and (resid 80 through 98 )
8X-RAY DIFFRACTION8chain 'D' and (resid 47 through 79 )
9X-RAY DIFFRACTION9chain 'D' and (resid 80 through 98 )
10X-RAY DIFFRACTION10chain 'E' and (resid 480 through 500 )

+
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