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- PDB-4x8n: Crystal structure of Ash2L SPRY domain in complex with phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 4x8n
TitleCrystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5
Components
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsPROTEIN BINDING / histone / MLL1 / chromatin / epigenetics
Function / homology
Function and homology information


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 / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling ...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 / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / 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 / beta-catenin binding / PKMTs methylate histone lysines / response to estrogen / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / transcription cis-regulatory region binding / positive regulation of cell population proliferation / DNA damage response / nucleolus / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. ...: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily / WD domain, G-beta repeat / Jelly Rolls / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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: 2.1 Å
AuthorsZhang, P. / Chaturvedi, C.P. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.-F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-136816 Canada
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 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Retinoblastoma-binding protein 5


Theoretical massNumber of molelcules
Total (without water)21,6712
Polymers21,6712
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.279, 51.542, 110.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 20322.094 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: 1349.228 Da / Num. of mol.: 1 / Fragment: UNP residues 347-356 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15291
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting 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: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→29.9 Å / Num. obs: 14095 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementResolution: 2.1→29.9 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2769 700 5.04 %
Rwork0.2133 --
obs0.2165 13895 97.17 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.234 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2831 Å20 Å20 Å2
2--0.3127 Å2-0 Å2
3---0.9704 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 213 1691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071542
X-RAY DIFFRACTIONf_angle_d1.0392087
X-RAY DIFFRACTIONf_dihedral_angle_d13.414568
X-RAY DIFFRACTIONf_chiral_restr0.078210
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20840.31621380.20662643X-RAY DIFFRACTION99
2.2084-2.43060.28611540.20582637X-RAY DIFFRACTION99
2.4306-2.7820.26631360.20772654X-RAY DIFFRACTION99
2.782-3.50420.26991320.21142653X-RAY DIFFRACTION97
3.5042-29.91710.26961400.22282608X-RAY DIFFRACTION91
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)
10.0049-0.0073-0.0030.01080.00330.00850.02280.1045-0.00630.0289-0.00880.002-0.09290.0201-0.00010.10030.0054-0.01750.10110.00740.1184-18.209622.239-22.5291
20.04330.0565-0.02140.0894-0.00160.05410.0143-0.05870.00330.0218-0.03580.05390.03690.019500.0852-0.0059-0.00470.0848-0.00540.0782-17.872610.0544-12.3163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 286:312 )A286 - 312
2X-RAY DIFFRACTION2( CHAIN A AND RESID 313:504 )A313 - 504

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