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- PDB-2xl2: WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE RECRUITED TO NOVEL SITE -

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Basic information

Entry
Database: PDB / ID: 2xl2
TitleWDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE RECRUITED TO NOVEL SITE
Components
  • 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 / Formation of the beta-catenin:TCF transactivating complex / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex ...Formation of WDR5-containing histone-modifying complexes / Formation of the beta-catenin:TCF transactivating complex / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / mitotic spindle / response to estrogen / neuron projection development / histone binding / transcription cis-regulatory region binding / regulation of cell cycle / DNA damage response / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Retinoblastoma-binding protein 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: RETINOBLASTOMA-BINDING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7228
Polymers76,3544
Non-polymers3684
Water3,387188
1
A: WD REPEAT-CONTAINING PROTEIN 5
C: RETINOBLASTOMA-BINDING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3614
Polymers38,1772
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5.8 kcal/mol
Surface area12180 Å2
MethodPISA
2
B: WD REPEAT-CONTAINING PROTEIN 5
D: RETINOBLASTOMA-BINDING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3614
Polymers38,1772
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5.2 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.440, 81.260, 87.520
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 31:334 )
211CHAIN B AND (RESSEQ 31:334 )
112CHAIN C AND (RESSEQ 5:14 )
212CHAIN D AND (RESSEQ 5:14 )

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.993557, 0.002602, 0.113304), (0.002411, -0.999995, 0.00182), (0.113308, -0.001535, -0.993559)
Vector: -2.5047, -14.36, 43.6011)

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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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON NATIVE TYROSINE AT AMINO TERMINUS

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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: 2.5 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M TRIS HCL PH 8.0, 25% PEG 8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 10, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→59.5 Å / Num. obs: 23706 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 31.16 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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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: 2.4→43.695 Å / SU ML: 0.34 / σ(F): 0.01 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 1206 5.1 %
Rwork0.1855 --
obs0.1884 23706 90.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.721 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-27.1514 Å2-0 Å2-5.1225 Å2
2---17.4712 Å20 Å2
3----9.6802 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 24 188 5076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075014
X-RAY DIFFRACTIONf_angle_d1.1286801
X-RAY DIFFRACTIONf_dihedral_angle_d15.4111757
X-RAY DIFFRACTIONf_chiral_restr0.086770
X-RAY DIFFRACTIONf_plane_restr0.004845
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2341X-RAY DIFFRACTIONPOSITIONAL
12B2341X-RAY DIFFRACTIONPOSITIONAL0.03
21C73X-RAY DIFFRACTIONPOSITIONAL
22D73X-RAY DIFFRACTIONPOSITIONAL0.118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.34231170.25362178X-RAY DIFFRACTION79
2.4961-2.60970.30291000.23122225X-RAY DIFFRACTION81
2.6097-2.74730.29991340.2152345X-RAY DIFFRACTION86
2.7473-2.91940.2821270.20732473X-RAY DIFFRACTION90
2.9194-3.14470.29031510.20012529X-RAY DIFFRACTION93
3.1447-3.46110.21711270.17492638X-RAY DIFFRACTION97
3.4611-3.96160.20821680.15872670X-RAY DIFFRACTION97
3.9616-4.99010.18461430.13062695X-RAY DIFFRACTION98
4.9901-43.70240.21271390.17252747X-RAY DIFFRACTION97

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