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- PDB-2w5y: Binary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain w... -

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Basic information

Entry
Database: PDB / ID: 2w5y
TitleBinary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine.
ComponentsHISTONE-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


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity / 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 / cellular response to transforming growth factor beta stimulus / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / visual learning / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / protein-containing complex assembly / methylation / chromatin binding / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / 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 / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / 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-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,6313
Polymers22,1811
Non-polymers4502
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.850, 56.210, 78.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: Chemical ChemComp-ZN / ZINC ION


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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5'-DEOXY-S-ADENOSYL-L-HOMOCYSTEINE (SAH): ADOHCY
Sequence detailsCONSTRUCT USED FOR CRYSTALLISATION CONTAINS RESIDUES 3785 TO 3969

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.8
Details: 0.1 M SODIUM CACODYLATE, PH6.5, 2 % PEG 8000, 30 % 2-METHYL-2,4-PENTANDIOL, pH 6.8

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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: Apr 13, 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→56.2 Å / Num. obs: 13868 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 27.77 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PEG

1peg


Resolution: 2→23.66 Å / SU ML: 0.3 / σ(F): 1.45 / Phase error: 23.94 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflection
Rfree0.264 1268 4.8 %
Rwork0.187 --
obs0.191 26312 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.61 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.94 Å2
Baniso -1Baniso -2Baniso -3
1--8.7679 Å2-0 Å20 Å2
2---4.7871 Å2-0 Å2
3---13.555 Å2
Refinement stepCycle: LAST / Resolution: 2→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 27 130 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081418
X-RAY DIFFRACTIONf_angle_d1.2661904
X-RAY DIFFRACTIONf_dihedral_angle_d19.338536
X-RAY DIFFRACTIONf_chiral_restr0.081198
X-RAY DIFFRACTIONf_plane_restr0.008246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.08030.2437910.22972048X-RAY DIFFRACTION69
2.0803-2.17490.24551430.22192394X-RAY DIFFRACTION82
2.1749-2.28950.29341480.20052895X-RAY DIFFRACTION98
2.2895-2.43280.27431610.18832968X-RAY DIFFRACTION99
2.4328-2.62040.27561540.1892954X-RAY DIFFRACTION99
2.6204-2.88370.23591370.17862961X-RAY DIFFRACTION99
2.8837-3.30.24631360.17442991X-RAY DIFFRACTION100
3.3-4.1540.25551630.16022957X-RAY DIFFRACTION100
4.154-23.65920.27211350.1952876X-RAY DIFFRACTION97

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