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- PDB-9c4u: Menin mutant T349M in complex with MLL peptide -

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Basic information

Entry
Database: PDB / ID: 9c4u
TitleMenin mutant T349M in complex with MLL peptide
Components
  • Histone-lysine N-methyltransferase 2A
  • Menin
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / Y-form DNA binding / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / Y-form DNA binding / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / MLL1/2 complex / negative regulation of JNK cascade / definitive hemopoiesis / histone H3K4 methyltransferase activity / osteoblast development / anterior/posterior pattern specification / T-helper 2 cell differentiation / embryonic hemopoiesis / exploration behavior / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / minor groove of adenine-thymine-rich DNA binding / cleavage furrow / MLL1 complex / negative regulation of cell cycle / negative regulation of protein phosphorylation / membrane depolarization / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / response to UV / four-way junction DNA binding / negative regulation of fibroblast proliferation / cellular response to transforming growth factor beta stimulus / spleen development / homeostasis of number of cells within a tissue / transcription repressor complex / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / : / response to gamma radiation / negative regulation of DNA-binding transcription factor activity / phosphoprotein binding / Post-translational protein phosphorylation / Deactivation of the beta-catenin transactivating complex / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / nuclear matrix / Transcriptional regulation of granulopoiesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-containing complex assembly / double-stranded DNA binding / fibroblast proliferation / protein-macromolecule adaptor activity / methylation / chromosome, telomeric region / transcription cis-regulatory region binding / endoplasmic reticulum lumen / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Menin / Menin / 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 ...Menin / Menin / 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. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / 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
DI(HYDROXYETHYL)ETHER / Menin / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.569 Å
AuthorsClegg, B.D. / Cierpicki, T. / Grembecka, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)272561 United States
CitationJournal: To Be Published
Title: Menin mutant T349M in complex with MLL peptide
Authors: Clegg, B.D. / Cierpicki, T. / Grembecka, J.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Menin
B: Histone-lysine N-methyltransferase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6267
Polymers56,0032
Non-polymers6235
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-20 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.045, 80.235, 125.085
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Menin


Mass: 54600.316 Da / Num. of mol.: 1 / Mutation: T349M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, SCG2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00255
#2: Protein/peptide Histone-lysine N-methyltransferase 2A / C-terminal cleavage product of 180 kDa / p180


Mass: 1402.607 Da / Num. of mol.: 1 / Mutation: C5A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03164

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Non-polymers , 6 types, 507 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 44.12 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.569→50 Å / Num. obs: 69845 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 20.952
Reflection shellResolution: 1.569→1.6 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3438

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000722data reduction
HKL-2000722data scaling
MOLREP11.0 / 22.07.2010phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.569→29.153 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.57 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1971 3548 5.085 %
Rwork0.1598 66223 -
all0.162 --
obs-69771 99.883 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.533 Å20 Å20 Å2
2---0.228 Å20 Å2
3----0.306 Å2
Refinement stepCycle: LAST / Resolution: 1.569→29.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 43 503 4281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163779
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.8255470
X-RAY DIFFRACTIONr_angle_other_deg0.6481.7438687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.145526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.46251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83110659
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.38610181
X-RAY DIFFRACTIONr_chiral_restr0.0980.2602
X-RAY DIFFRACTIONr_chiral_restr_other0.0010.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
X-RAY DIFFRACTIONr_nbd_refined0.2280.2839
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23387
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21983
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.214
X-RAY DIFFRACTIONr_nbd_other0.1850.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.228
X-RAY DIFFRACTIONr_mcbond_it1.8631.5761994
X-RAY DIFFRACTIONr_mcbond_other1.861.5761994
X-RAY DIFFRACTIONr_mcangle_it2.7712.8172514
X-RAY DIFFRACTIONr_mcangle_other2.772.8192515
X-RAY DIFFRACTIONr_scbond_it2.9051.8572028
X-RAY DIFFRACTIONr_scbond_other2.9051.8572029
X-RAY DIFFRACTIONr_scangle_it4.3673.2542956
X-RAY DIFFRACTIONr_scangle_other4.3673.2542957
X-RAY DIFFRACTIONr_lrange_it5.95919.034766
X-RAY DIFFRACTIONr_lrange_other5.80517.7644634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.569-1.610.2722380.24747860.24850870.9520.9698.76150.229
1.61-1.6540.2442450.22146920.22249370.9610.9681000.197
1.654-1.7020.2512260.20346100.20548360.9640.9731000.179
1.702-1.7540.2172340.18544700.18647040.9710.9771000.158
1.754-1.8110.2162490.17543020.17745510.9720.981000.149
1.811-1.8750.2152470.16741390.1743860.9710.9811000.143
1.875-1.9450.1992200.1740350.17142550.9750.9821000.147
1.945-2.0240.2221960.16739130.16941090.9670.9821000.148
2.024-2.1140.1881960.1537680.15239640.9780.9861000.135
2.114-2.2160.1671790.14135790.14237580.9810.9881000.128
2.216-2.3350.1591850.13234410.13436260.9830.9891000.121
2.335-2.4760.21650.13532360.13834010.9770.9881000.125
2.476-2.6460.181690.13930360.14132050.9780.9881000.131
2.646-2.8560.1761560.14928700.1530260.9790.9861000.144
2.856-3.1250.1951510.16226360.16427870.9790.9841000.16
3.125-3.4890.2251200.16724190.1725390.970.9841000.171
3.489-4.0190.1521340.13721040.13822380.9860.9891000.146
4.019-4.8990.1841010.13718370.1419380.9830.9891000.149
4.899-6.8330.229870.18714530.1915400.9790.9851000.204
6.833-29.1530.231500.1838980.1859500.9780.98399.78950.211

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