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- PDB-2h68: Histone H3 recognition and presentation by the WDR5 module of the... -

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Basic information

Entry
Database: PDB / ID: 2h68
TitleHistone H3 recognition and presentation by the WDR5 module of the MLL1 complex
ComponentsWD-repeat protein 5
KeywordsGENE REGULATION / WD40 WD-repeat histone modification chromatin
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / 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 / nucleoplasm / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRuthenburg, A.J. / Wang, W.-K. / Graybosch, D.M. / Li, H. / Allis, C.D. / Patel, D.J. / Verdine, G.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.
Authors: Ruthenburg, A.J. / Wang, W.-K. / Graybosch, D.M. / Li, H. / Allis, C.D. / Patel, D.J. / Verdine, G.L.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: WD-repeat protein 5
B: WD-repeat protein 5


Theoretical massNumber of molelcules
Total (without water)68,6082
Polymers68,6082
Non-polymers00
Water10,467581
1
A: WD-repeat protein 5


Theoretical massNumber of molelcules
Total (without water)34,3041
Polymers34,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD-repeat protein 5


Theoretical massNumber of molelcules
Total (without water)34,3041
Polymers34,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.591, 46.359, 112.369
Angle α, β, γ (deg.)90.00, 117.15, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is one protomer of the two in the assymetric unit.

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Components

#1: Protein WD-repeat protein 5 / BMP2-induced 3-kb gene protein


Mass: 34303.914 Da / Num. of mol.: 2 / Fragment: residues 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P61964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growDetails: Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) ...Details: Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2005 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.79→37.2 Å / Num. obs: 57801 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.9
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 7.5 / Num. unique all: 5760 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERJ

1erj


Resolution: 1.79→37.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.914 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.121 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19198 2926 5.1 %RANDOM
Rwork0.16575 ---
all0.178 57801 --
obs0.1671 54493 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.27 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 0 581 5304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224836
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.946563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59925.243185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54615835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.166156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023552
X-RAY DIFFRACTIONr_nbd_refined0.2020.22180
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2486
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.247
X-RAY DIFFRACTIONr_mcbond_it0.7651.53105
X-RAY DIFFRACTIONr_mcangle_it1.28224895
X-RAY DIFFRACTIONr_scbond_it2.15332030
X-RAY DIFFRACTIONr_scangle_it3.3394.51668
LS refinement shellResolution: 1.791→1.838 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 195 -
Rwork0.16 3544 -
obs--87.44 %
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)
10.3464-0.0964-0.12310.2733-0.0770.17080.01630.0264-0.0432-0.0024-0.0250.0023-0.0173-0.01480.0087-0.00480.0023-0.0175-0.0145-0.0135-0.02091.34640.906633.4938
20.29210.0238-0.0860.31110.15820.2989-0.0139-0.0066-0.0071-0.0127-0.01110.0117-0.01240.00430.025-0.00460.0114-0.0199-0.02360.0028-0.0191-25.826723.032416.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 3349 - 312
2X-RAY DIFFRACTION2BB29 - 3347 - 312

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