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- PDB-4rta: Cystal structure of the Dpy30 for MLL/SET1 COMPASS H3K4 trimethylation -

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Basic information

Entry
Database: PDB / ID: 4rta
TitleCystal structure of the Dpy30 for MLL/SET1 COMPASS H3K4 trimethylation
ComponentsProtein dpy-30 homolog
KeywordsPROTEIN BINDING / Rossmann Fold / h3k4 methylation / Ash2L
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / transcription initiation-coupled chromatin remodeling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / trans-Golgi network ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / transcription initiation-coupled chromatin remodeling / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Protein dpy-30 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 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 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4755
Polymers24,3372
Non-polymers1383
Water1,02757
1
A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
hetero molecules

A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,95110
Polymers48,6754
Non-polymers2766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
Unit cell
Length a, b, c (Å)89.579, 89.579, 53.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 12168.677 Da / Num. of mol.: 2
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) / References: UniProt: Q9C005
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.9
Details: 0.1M COCADYLATE SODIUM, SODIUM FORMATE 4.2M, pH 5.9, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.123→30 Å / Num. all: 12723 / Num. obs: 12673 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 24.8
Reflection shellResolution: 2.123→2.21 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 5 / Rsym value: 0.47 / % possible all: 100

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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: 2.123→27.214 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 618 4.9 %
Rwork0.2067 --
obs0.2081 12624 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.123→27.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 9 57 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071123
X-RAY DIFFRACTIONf_angle_d1.0271523
X-RAY DIFFRACTIONf_dihedral_angle_d17.046450
X-RAY DIFFRACTIONf_chiral_restr0.042177
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1226-2.33610.25671460.24572918X-RAY DIFFRACTION99
2.3361-2.67390.28651510.232977X-RAY DIFFRACTION100
2.6739-3.36790.24981660.22312993X-RAY DIFFRACTION100
3.3679-27.21620.21291550.18833118X-RAY DIFFRACTION98
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)
12.0292.55160.97042.01980.75627.9079-0.73031.5422-0.6415-0.48120.5893-0.27790.17970.80130.02190.4189-0.0178-0.04040.6573-0.110.44860.778326.4956-15.1215
22.03825.54573.57394.7903-3.64519.3883-0.13120.1623-0.3431-0.0538-0.02180.3467-0.311-0.08380.21040.24630.0504-0.00720.3157-0.01560.33033.692229.97-5.6742
36.89131.8511.40986.13583.69068.35710.2508-0.4855-0.90280.9058-0.0504-0.33710.8889-0.1764-0.22330.37570.0105-0.03710.22760.07620.352912.806125.8768.8814
48.16133.15876.79332.09641.88429.72220.4930.3368-2.06160.1066-0.497-1.49612.0031-0.91070.00020.5743-0.0482-0.03790.6802-0.18341.17052.284918.2878-4.8477
50.60350.6964-1.1970.9897-1.53132.50530.271-0.09230.66360.9192-0.15921.1494-0.4736-0.7548-0.05571.0877-0.08310.00681.1438-0.33251.30979.418749.395417.267
62.16442.7345-9.88112.23296.86222.06330.239-0.53810.47580.4370.2114-0.22640.81710.2305-0.46660.4250.011-0.06940.3335-0.03050.320414.842239.274913.2248
79.54770.1243.51828.60671.51459.21420.11510.7996-0.357-0.27640.0327-0.87390.01960.5408-0.10770.20450.04530.07710.2743-0.01320.31316.860629.7231-3.7792
82.0411.9904-3.58432.01268.32752.0194-0.0231-1.0694-0.23151.51911-2.42481.14942.5631-0.85110.74410.1519-0.09790.6624-0.10881.034826.110439.35069.6849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 45 THROUGH 52 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 53 THROUGH 61 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 62 THROUGH 94 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 95 THROUGH 102 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 24 THROUGH 47 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 48 THROUGH 61 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 62 THROUGH 95 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 96 THROUGH 102 )

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