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- PDB-3psl: Fine-tuning the stimulation of MLL1 methyltransferase activity by... -

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Basic information

Entry
Database: PDB / ID: 3psl
TitleFine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3 based peptide mimetic
Components
  • N-alpha acetylated form of histone H3
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / chromatin / histone / beta-propeller / scaffolding / RbBP5 / MLL1 / nucleus / TRANSCRIPTION - TRANSCRIPTION INHIBITOR complex / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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: 1.7 Å
AuthorsAvdic, V. / Zhang, P. / Lanouette, S. / Voronova, A. / Skerjanc, I. / Couture, J.-F.
CitationJournal: Faseb J. / Year: 2011
Title: Fine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3-based peptide mimetic.
Authors: Avdic, V. / Zhang, P. / Lanouette, S. / Voronova, A. / Skerjanc, I. / Couture, J.F.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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: N-alpha acetylated form of histone H3
D: N-alpha acetylated form of histone H3


Theoretical massNumber of molelcules
Total (without water)70,8504
Polymers70,8504
Non-polymers00
Water6,323351
1
A: WD repeat-containing protein 5
C: N-alpha acetylated form of histone H3


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area11260 Å2
MethodPISA
2
B: WD repeat-containing protein 5
D: N-alpha acetylated form of histone H3


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-4 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.947, 48.614, 63.308
Angle α, β, γ (deg.)98.79, 90.95, 117.48
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 34794.449 Da / Num. of mol.: 2 / Fragment: WDR5 (unp residues 21-334)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide N-alpha acetylated form of histone H3


Mass: 630.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-alpha acetylated form of histone H3 (synthetic)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.74 Å3/Da / Density % sol: 29.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50 mM NaAcetate, 100 mM NH4 SO4 , and 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.023 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.023 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 51999 / Num. obs: 50439 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rsym value: 0.065 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.232 / % possible all: 93.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H14

2h14


Resolution: 1.7→35.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.835 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2575 5.1 %RANDOM
Rwork0.15492 ---
all0.193 50439 --
obs0.15747 47864 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0.01 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 0 351 5016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224774
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9376468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5245598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90924.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31115816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.248158
X-RAY DIFFRACTIONr_chiral_restr0.1620.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213482
X-RAY DIFFRACTIONr_mcbond_it1.2941.52998
X-RAY DIFFRACTIONr_mcangle_it2.17324831
X-RAY DIFFRACTIONr_scbond_it3.42731776
X-RAY DIFFRACTIONr_scangle_it5.3414.51637
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 172 -
Rwork0.199 3244 -
obs--89.28 %
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)
10.6079-0.19610.16340.52920.06620.218-0.0163-0.02070.0385-0.02660.0091-0.02620.0081-0.00820.00710.0277-0.007800.0408-0.0020.0416-10.775117.772411.5123
20.52620.1781-0.21571.25380.26120.5077-0.10350.06420.00450.24130.11230.03660.11110.0871-0.00880.10070.01880.00990.04740.00080.002110.74433.954443.0744
32.9797-1.4463-2.55222.36632.6933.46350.1064-0.1222-0.01150.0946-0.1333-0.02430.0357-0.09170.02690.04940.0027-0.02520.0814-0.00560.0707-17.827215.934821.6816
44.0985-0.63382.9684.2579-0.84592.9485-0.0170.0366-0.0511-0.11870.04570.1269-0.0519-0.0242-0.02870.0498-0.0058-0.00370.04790.01220.04883.39396.876932.9315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 334
2X-RAY DIFFRACTION2B32 - 334
3X-RAY DIFFRACTION3C0 - 4
4X-RAY DIFFRACTION4D0 - 4

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