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- PDB-9c4v: Menin mutant G331D in complex with MLL peptide -

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Basic information

Entry
Database: PDB / ID: 9c4v
TitleMenin mutant G331D 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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / Y-form DNA binding / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL1/2 complex ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / Y-form DNA binding / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL1/2 complex / definitive hemopoiesis / regulation of short-term neuronal synaptic plasticity / histone H3K4 methyltransferase activity / osteoblast development / anterior/posterior pattern specification / negative regulation of JNK cascade / T-helper 2 cell differentiation / embryonic hemopoiesis / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / exploration behavior / minor groove of adenine-thymine-rich DNA binding / histone methyltransferase complex / negative regulation of cell cycle / R-SMAD binding / cleavage furrow / MLL1 complex / membrane depolarization / negative regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / : / RHO GTPases activate IQGAPs / negative regulation of fibroblast proliferation / response to UV / spleen development / four-way junction DNA binding / transcription repressor complex / transcription initiation-coupled chromatin remodeling / homeostasis of number of cells within a tissue / Transferases; Transferring one-carbon groups; Methyltransferases / response to gamma radiation / post-embryonic development / Post-translational protein phosphorylation / circadian regulation of gene expression / Deactivation of the beta-catenin transactivating complex / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Transcriptional regulation of granulopoiesis / 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 profile. / SET domain superfamily / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Menin / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: J.Biol.Chem. / Year: 2024
Title: Drug-resistant menin variants retain high binding affinity and interactions with MLL1.
Authors: Ray, J. / Clegg, B. / Grembecka, J. / Cierpicki, T.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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)56,7408
Polymers56,0312
Non-polymers7096
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-49 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.082, 80.217, 124.926
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 AB

#1: Protein Menin


Mass: 54628.258 Da / Num. of mol.: 1 / Mutation: G331D
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 , 5 types, 535 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


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


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


Mass: 18.015 Da / Num. of mol.: 529 / 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: 44.05 %
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: 1.469→50 Å / Num. obs: 84613 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 33.083
Reflection shellResolution: 1.469→1.5 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4171

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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: 1.47→27.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.198 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.188 4080 4.826 %
Rwork0.16 --
obs-84536 99.7 %
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: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.279 Å20 Å20 Å2
2---0.059 Å20 Å2
3----0.219 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 38 531 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123963
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163714
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.8245386
X-RAY DIFFRACTIONr_angle_other_deg0.6691.7498534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.823527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99910646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02938
X-RAY DIFFRACTIONr_nbd_refined0.230.2810
X-RAY DIFFRACTIONr_nbd_other0.1450.271
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21976
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1091.8091965
X-RAY DIFFRACTIONr_mcbond_other2.111.8091965
X-RAY DIFFRACTIONr_mcangle_it3.0373.2372469
X-RAY DIFFRACTIONr_mcangle_other3.0363.2392470
X-RAY DIFFRACTIONr_scbond_it3.2462.1071998
X-RAY DIFFRACTIONr_scbond_other3.2472.1081999
X-RAY DIFFRACTIONr_scangle_it4.8473.7162917
X-RAY DIFFRACTIONr_scangle_other4.8463.7172918
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 302 -
Rwork0.251 5660 -
obs--96.71 %

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