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- PDB-4x8p: Crystal structure of Ash2L SPRY domain in complex with RbBP5 -

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Basic information

Entry
Database: PDB / ID: 4x8p
TitleCrystal structure of Ash2L SPRY domain in complex with RbBP5
Components
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsPROTEIN BINDING / histone / MLL1 / epigenetics
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / Neddylation / histone binding / transcription cis-regulatory region binding / DNA damage response / positive regulation of cell population proliferation / nucleolus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / SPRY domain / Retinoblastoma-binding protein 5/Swd1 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...: / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / SPRY domain / Retinoblastoma-binding protein 5/Swd1 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / Jelly Rolls / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Retinoblastoma-binding protein 5 / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsZhang, P. / Chaturvedi, C.P. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.-F.
CitationJournal: Genes Dev. / Year: 2015
Title: A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation.
Authors: Zhang, P. / Chaturvedi, C.P. / Tremblay, V. / Cramet, M. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.F.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0773
Polymers21,9852
Non-polymers921
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-4 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.500, 59.100, 70.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


Mass: 20409.172 Da / Num. of mol.: 1 / Fragment: UNP residues 380-495, 539-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBL3
#2: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 1575.563 Da / Num. of mol.: 1 / Fragment: UNP residues 344-355 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15291
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→29.6 Å / Num. obs: 11628 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.54 Å2 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementResolution: 2.2→29.17 Å / Cor.coef. Fo:Fc: 0.9168 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.311 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.271 537 4.78 %RANDOM
Rwork0.2199 ---
obs0.2223 11232 98.19 %-
Displacement parametersBiso mean: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.7524 Å20 Å20 Å2
2---0.8622 Å20 Å2
3---1.6147 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: 1 / Resolution: 2.2→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 6 122 1611
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011530HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052068HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d504SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes224HARMONIC5
X-RAY DIFFRACTIONt_it1530HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion16.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion186SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1862SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.41 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3554 130 4.95 %
Rwork0.2629 2498 -
all0.2671 2628 -
obs--98.19 %

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