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- PDB-4rt4: Crystal structure of Dpy30 complexed with Bre2 -

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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 / : / Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex ...Formation of WDR5-containing histone-modifying complexes / : / Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / MLL1 complex / subtelomeric heterochromatin formation / telomere maintenance / transcription initiation-coupled chromatin remodeling / trans-Golgi network / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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 / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain ...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 / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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 )

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