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- PDB-2w5z: Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain ... -

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Basic information

Entry
Database: PDB / ID: 2w5z
TitleTernary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide.
Components
  • HISTONE PEPTIDE
  • HISTONE-LYSINE N-METHYLTRANSFERASE HRX
KeywordsTRANSFERASE / TRANSCRIPTION REGULATION / CHROMOSOMAL REARRANGEMENT / PROTEIN LYSINE METHYLTRANSFERASE / PROTO-ONCOGENE / PHOSPHOPROTEIN / UBL CONJUGATION / S-ADENOSYL-L-METHIONINE / MIXED LINEAGE LEUKAEMIA / POLYMORPHISM / TRANSCRIPTION / METAL-BINDING / ZINC-FINGER / DNA-BINDING / BROMODOMAIN / METHYLTRANSFERASE / CHROMATIN REGULATOR / ALTERNATIVE SPLICING / HISTONE MODIFICATION / MLL1 / ZINC / KMT2A / NUCLEUS / APOPTOSIS / SET DOMAIN
Function / homology
Function and homology information


Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / protein-cysteine methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / response to potassium ion ...Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / protein-cysteine methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / : / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / fibroblast proliferation / protein-containing complex assembly / protein heterodimerization activity / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / PHD-finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3.1 / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSouthall, S.M. / Wong, P.S. / Odho, Z. / Roe, S.M. / Wilson, J.R.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Basis for the Requirement of Additional Factors for Mll1 Set Domain Activity and Recognition of Epigenetic Marks.
Authors: Southall, S.M. / Wong, P.S. / Odho, Z. / Roe, S.M. / Wilson, J.R.
History
DepositionDec 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE-LYSINE N-METHYLTRANSFERASE HRX
C: HISTONE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9406
Polymers23,3062
Non-polymers6344
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7.1 kcal/mol
Surface area14110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.950, 56.550, 78.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE HRX / ZINC FINGER PROTEIN HRX / ALL-1 / TRITHORAX-LIKE PROTEIN / LYSINE N-METHYLTRANSFERASE 2A / CXXC- ...ZINC FINGER PROTEIN HRX / ALL-1 / TRITHORAX-LIKE PROTEIN / LYSINE N-METHYLTRANSFERASE 2A / CXXC-TYPE ZINC FINGER PROTEIN 7 / MLL-1


Mass: 22181.402 Da / Num. of mol.: 1 / Fragment: METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTHREE-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q03164, histone-lysine N-methyltransferase
#2: Protein/peptide HISTONE PEPTIDE


Mass: 1124.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTHREE-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: P68433*PLUS, histone-lysine N-methyltransferase

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Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details5'-DEOXY-S-ADENOSYL-L-HOMOCYSTEINE (SAH): ADOHCY
Sequence detailsCONSTRUCT USED FOR CRYSTALLISATION CONTAINS RESIDUES 3785 TO 3969 REISDUES 1 TO 8 C-TERMINAL TYR ...CONSTRUCT USED FOR CRYSTALLISATION CONTAINS RESIDUES 3785 TO 3969 REISDUES 1 TO 8 C-TERMINAL TYR ADDED AT POSITION 9

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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: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.8
Details: 0.1 M SODIUM CACODYLATE PH6.8, 2 % PEG 5000, 30 % 2-METHYL-2, 4-PENTANDIOL

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHIC CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→41.5 Å / Num. obs: 20973 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.52 Å / SU ML: 0.31 / σ(F): 1.26 / Phase error: 26.58 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflection
Rfree0.247 1080 5.2 %
Rwork0.194 --
obs0.197 20973 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.8 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43.13 Å2
Baniso -1Baniso -2Baniso -3
1--18.6654 Å2-0 Å20 Å2
2---13.6174 Å2-0 Å2
3---5.6224 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 39 64 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051595
X-RAY DIFFRACTIONf_angle_d0.9112151
X-RAY DIFFRACTIONf_dihedral_angle_d17.11631
X-RAY DIFFRACTIONf_chiral_restr0.073219
X-RAY DIFFRACTIONf_plane_restr0.003281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.30030.2971270.22092280X-RAY DIFFRACTION91
2.3003-2.42160.31621240.24092549X-RAY DIFFRACTION100
2.4216-2.57330.34681360.2282539X-RAY DIFFRACTION99
2.5733-2.77190.26491350.20562480X-RAY DIFFRACTION99
2.7719-3.05080.25611490.18862503X-RAY DIFFRACTION100
3.0508-3.49210.26581420.17812512X-RAY DIFFRACTION99
3.4921-4.39890.15641220.14952549X-RAY DIFFRACTION100
4.3989-41.53030.21261450.17622481X-RAY DIFFRACTION99

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