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- PDB-2xl3: WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 2xl3
TitleWDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE
Components
  • HISTONE H3.1Histone H3
  • RETINOBLASTOMA-BINDING PROTEIN 5
  • WD REPEAT-CONTAINING PROTEIN 5
KeywordsTRANSCRIPTION / MLL COMPLEX / H3K4 METHYLATION / WD-40 BETA-PROPELLER
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines ...Formation of WDR5-containing histone-modifying complexes / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / mitotic spindle / structural constituent of chromatin / response to estrogen / neuron projection development / nucleosome / chromatin organization / histone binding / transcription cis-regulatory region binding / regulation of cell cycle / protein heterodimerization activity / DNA damage response / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 ...Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone H3.1 / Retinoblastoma-binding protein 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOdho, Z. / Southall, S.M. / Wilson, J.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Characterisation of a Novel Wdr5 Binding Site that Recruits Rbbp5 Through a Conserved Motif and Enhances Methylation of H3K4 by Mll1.
Authors: Odho, Z. / Southall, S.M. / Wilson, J.R.
History
DepositionJul 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: WD REPEAT-CONTAINING PROTEIN 5
B: WD REPEAT-CONTAINING PROTEIN 5
C: RETINOBLASTOMA-BINDING PROTEIN 5
D: HISTONE H3.1
E: RETINOBLASTOMA-BINDING PROTEIN 5
F: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8259
Polymers78,5486
Non-polymers2763
Water1,928107
1
A: WD REPEAT-CONTAINING PROTEIN 5
C: RETINOBLASTOMA-BINDING PROTEIN 5
D: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4585
Polymers39,2743
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-4.1 kcal/mol
Surface area11970 Å2
MethodPISA
2
B: WD REPEAT-CONTAINING PROTEIN 5
E: RETINOBLASTOMA-BINDING PROTEIN 5
F: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3664
Polymers39,2743
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-8.3 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.100, 81.320, 86.350
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 32:334 )
211CHAIN B AND (RESSEQ 32:334 )

NCS oper: (Code: given
Matrix: (0.998316, -0.000389, 0.058006), (-0.000425, -1, 0.00061), (0.058006, -0.000634, -0.998316)
Vector: -1.51768, 15.4442, 41.6984)

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Components

#1: Protein WD REPEAT-CONTAINING PROTEIN 5 / WDR5 / BMP2-INDUCED 3-KB GENE PROTEIN / WD REPEAT-CONTAINING PROTEIN BIG-3


Mass: 36635.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61965
#2: Protein/peptide RETINOBLASTOMA-BINDING PROTEIN 5 / RBBP5 / RBBP-5


Mass: 1541.524 Da / Num. of mol.: 2 / Fragment: RESIDUES 369-381 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q8BX09
#3: Protein/peptide HISTONE H3.1 / Histone H3


Mass: 1097.248 Da / Num. of mol.: 2 / Fragment: AMINO TERMINAL TAIL, RESIDUES 2-9 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P68433
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON NATIVE CARBOXY TERMINAL TYROSINE NON NATIVE TYROSINE AT AMINO TERMINAL

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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: 2.45 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growpH: 8 / Details: 0.2M K2SO4 20 % PEG 3350, pH 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→86.3 Å / Num. obs: 16657 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H13

2h13


Resolution: 2.7→41.688 Å / SU ML: 0.3 / σ(F): 0.02 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 832 5 %
Rwork0.1759 --
obs0.179 16657 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.69 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-31.1702 Å2-0 Å2-8.0183 Å2
2---23.2776 Å20 Å2
3----7.8926 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 18 107 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075027
X-RAY DIFFRACTIONf_angle_d1.16822
X-RAY DIFFRACTIONf_dihedral_angle_d16.0711748
X-RAY DIFFRACTIONf_chiral_restr0.073777
X-RAY DIFFRACTIONf_plane_restr0.003850
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2326X-RAY DIFFRACTIONPOSITIONAL
12B2326X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.86910.29451400.21312346X-RAY DIFFRACTION84
2.8691-3.09060.25621240.19992511X-RAY DIFFRACTION88
3.0906-3.40150.29631380.17672627X-RAY DIFFRACTION92
3.4015-3.89340.21831170.16192768X-RAY DIFFRACTION96
3.8934-4.9040.19911540.13392777X-RAY DIFFRACTION98
4.904-41.69280.20921590.17932796X-RAY DIFFRACTION96

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