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- PDB-7u5v: Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domai... -

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Basic information

Entry
Database: PDB / ID: 7u5v
TitleCrystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and Borealin peptide
Components
  • Borealin
  • Histone-lysine N-methyltransferase 2A
KeywordsGENE REGULATION / MLL1-SET / Borealin / Histone methyltransferase / Non-histone substrate
Function / homology
Function and homology information


positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / protein-cysteine methyltransferase activity / chromocenter / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity ...positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / protein-cysteine methyltransferase activity / chromocenter / 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 / chromosome passenger complex / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / mitotic metaphase chromosome alignment / intercellular bridge / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / membrane depolarization / SUMOylation of DNA replication proteins / MLL1 complex / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / chromosome organization / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of fibroblast proliferation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Resolution of Sister Chromatid Cohesion / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / RHO GTPases Activate Formins / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / Separation of Sister Chromatids / microtubule cytoskeleton / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / midbody / fibroblast proliferation / methylation / protein-containing complex assembly / apoptotic process / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax ...Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / 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. / 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. / 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
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2A / Borealin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.59 Å
AuthorsAn, S. / Cho, U.S. / Oh, H. / Sha, L. / Xu, J. / Kim, S. / Yang, W. / An, W. / Dou, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 R01 CA 250329-01 United States
CitationJournal: Nat.Cell Biol. / Year: 2023
Title: Non-canonical MLL1 activity regulates centromeric phase separation and genome stability.
Authors: Sha, L. / Yang, Z. / An, S. / Yang, W. / Kim, S. / Oh, H. / Xu, J. / Yin, J. / Wang, H. / Lenz, H.J. / An, W. / Cho, U.S. / Dou, Y.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2A
C: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5434
Polymers19,0932
Non-polymers4502
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-28 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.480, 54.480, 105.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Histone-lysine N-methyltransferase 2A / Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed- ...Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed-lineage leukemia / Myeloid/lymphoid or mixed-lineage leukemia protein 1 / Trithorax-like protein / Zinc finger protein HRX


Mass: 18002.770 Da / Num. of mol.: 1 / Fragment: SET Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03164
#2: Protein/peptide Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 1090.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q53HL2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12705 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12705 Å / Relative weight: 1
ReflectionResolution: 2.59→47.18 Å / Num. obs: 5905 / % possible obs: 97.96 % / Redundancy: 5.7 % / Biso Wilson estimate: 61.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.046 / Rrim(I) all: 0.114 / Rsym value: 0.046 / Net I/σ(I): 11.2
Reflection shellResolution: 2.59→2.63 Å / Rmerge(I) obs: 1.169 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 236 / CC1/2: 0.302 / Rpim(I) all: 0.789 / Rsym value: 0.789 / % possible all: 79.46

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 2.59→43.08 Å / SU ML: 0.1688 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3036 297 5.05 %
Rwork0.2477 5581 -
obs-5878 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.91 Å2
Refinement stepCycle: LAST / Resolution: 2.59→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 27 0 1027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951045
X-RAY DIFFRACTIONf_angle_d1.14971405
X-RAY DIFFRACTIONf_chiral_restr0.0641151
X-RAY DIFFRACTIONf_plane_restr0.0119178
X-RAY DIFFRACTIONf_dihedral_angle_d17.886164
LS refinement shellResolution: 2.59→2.68 Å
RfactorNum. reflection% reflection
Rfree0.479 139 -
Rwork0.4439 453 -
obs--83 %
Refinement TLS params.Method: refined / Origin x: -24.6494372563 Å / Origin y: 20.1590568478 Å / Origin z: 7.21096046363 Å
111213212223313233
T0.300492514873 Å20.0371559909795 Å20.00626106392673 Å2-0.414145635488 Å20.063026123167 Å2--0.39416146211 Å2
L7.72542453931 °20.509607534901 °22.72878907191 °2-1.85137810996 °20.89118991675 °2--4.88224288024 °2
S0.35207304696 Å °-0.81243000695 Å °-0.585836959307 Å °0.0554541856097 Å °-0.192340079679 Å °-0.000773090479248 Å °0.327925537825 Å °-0.440329030408 Å °-0.153653528524 Å °
Refinement TLS groupSelection details: all

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