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- PDB-2h6n: Histone H3 recognition and presentation by the WDR5 module of the... -

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Basic information

Entry
Database: PDB / ID: 2h6n
TitleHistone H3 recognition and presentation by the WDR5 module of the MLL1 complex
Components
  • Histone H3 K4-Me2 9-residue peptide
  • WD-repeat protein 5
KeywordsGENE REGULATION / WD40 WD-repeat histone modification MLL SET chromatin
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / mitotic spindle / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
WDR5 beta-propeller domain / 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. / WD40 repeats ...WDR5 beta-propeller domain / 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. / 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: 1.5 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 31, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
C: Histone H3 K4-Me2 9-residue peptide
D: Histone H3 K4-Me2 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)70,7884
Polymers70,7884
Non-polymers00
Water11,385632
1
A: WD-repeat protein 5
C: Histone H3 K4-Me2 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)35,3942
Polymers35,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-3 kcal/mol
Surface area11920 Å2
MethodPISA
2
B: WD-repeat protein 5
D: Histone H3 K4-Me2 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)35,3942
Polymers35,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-3 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.745, 46.131, 112.694
Angle α, β, γ (deg.)90.00, 117.17, 90.00
Int Tables number5
Space group name H-MC121

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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: Protein/peptide Histone H3 K4-Me2 9-residue peptide


Mass: 1090.300 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: the peptide was chemically synthesized using solid phase synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
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: ALS / Beamline: 5.0.2 / Wavelength: 0.9871 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9871 Å / Relative weight: 1
ReflectionResolution: 1.5→43.4 Å / Num. all: 98522 / Num. obs: 90444 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 9.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.86 / Num. unique all: 9750 / % possible all: 99.6

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Processing

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

1erj


Resolution: 1.5→43.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.444 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.078 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19766 5610 5.8 %RANDOM
Rwork0.17852 ---
all0.188 96032 --
obs0.17964 90444 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.08 Å2
2--0.34 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 0 632 5485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224966
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9426733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24625192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0461510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023640
X-RAY DIFFRACTIONr_nbd_refined0.1960.22176
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23423
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2474
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.245
X-RAY DIFFRACTIONr_mcbond_it0.731.53175
X-RAY DIFFRACTIONr_mcangle_it1.16525014
X-RAY DIFFRACTIONr_scbond_it1.91432082
X-RAY DIFFRACTIONr_scangle_it2.9554.51719
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 376 -
Rwork0.206 5779 -
obs--84 %
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)
10.439-0.1557-0.26150.4096-0.03170.25790.02030.0227-0.0544-0.0515-0.07290.0365-0.0154-0.02370.0527-0.00430.0165-0.0212-0.0279-0.0209-0.00871.13630.943133.6061
20.4705-0.0523-0.18820.31830.18660.3922-0.02290.0092-0.01640.0416-0.0115-0.0358-0.0037-0.01330.0344-0.00460.003-0.0255-0.03570.0074-0.0122-26.054323.173716.2718
30.4603-0.39240.14714.16731.41111.9511-0.0696-0.20180.10380.17830.028-0.05010.0074-0.05540.0416-0.0049-0.0034-0.0009-0.02250.0024-0.028411.35264.793843.8165
40.56780.67060.73124.3353-0.65261.5904-0.16580.15190.0839-0.14410.03970.0396-0.0308-0.05590.1261-0.00480.01970.00780.0151-0.0075-0.0428-36.686327.16016.4209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 3349 - 312
2X-RAY DIFFRACTION2BB30 - 3348 - 312
3X-RAY DIFFRACTION3CC1 - 81 - 8
4X-RAY DIFFRACTION4DD1 - 81 - 8

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