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- PDB-9c4x: Menin mutant - M327I -

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Basic information

Entry
Database: PDB / ID: 9c4x
TitleMenin mutant - M327I
ComponentsMenin
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


negative regulation of cyclin-dependent protein serine/threonine kinase activity / Y-form DNA binding / MLL1/2 complex / osteoblast development / negative regulation of JNK cascade / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / histone methyltransferase complex ...negative regulation of cyclin-dependent protein serine/threonine kinase activity / Y-form DNA binding / MLL1/2 complex / osteoblast development / negative regulation of JNK cascade / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / histone methyltransferase complex / negative regulation of cell cycle / R-SMAD binding / cleavage furrow / MLL1 complex / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / : / response to UV / four-way junction DNA binding / transcription repressor complex / transcription initiation-coupled chromatin remodeling / response to gamma radiation / Post-translational protein phosphorylation / Deactivation of the beta-catenin transactivating complex / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / double-stranded DNA binding / protein-macromolecule adaptor activity / 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 / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DI(HYDROXYETHYL)ETHER / Menin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.577 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

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Assembly

Deposited unit
A: Menin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3557
Polymers54,5521
Non-polymers8036
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49, 80.203, 124.65
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Menin


Mass: 54552.184 Da / Num. of mol.: 1 / Mutation: M327I
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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.21 %
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: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.577→50 Å / Num. obs: 67731 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.49
Reflection shellResolution: 1.577→1.61 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3251

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000722data reduction
HKL-2000722data scaling
MOLREP11.0 / 22.07.2010/phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.577→31.182 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.155 / SU B: 1.526 / SU ML: 0.053 / Average fsc free: 0.9731 / Average fsc work: 0.9804 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1939 3367 4.976 %
Rwork0.1613 64300 -
all0.163 --
obs-67667 98.738 %
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: 19.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.425 Å20 Å20 Å2
2--0.596 Å20 Å2
3----2.021 Å2
Refinement stepCycle: LAST / Resolution: 1.577→31.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 52 449 4173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163654
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.8265235
X-RAY DIFFRACTIONr_angle_other_deg0.6451.7428407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.443526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2610632
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.36810173
X-RAY DIFFRACTIONr_chiral_restr0.10.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
X-RAY DIFFRACTIONr_nbd_refined0.2370.2772
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23310
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21923
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.210
X-RAY DIFFRACTIONr_nbd_other0.1660.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.229
X-RAY DIFFRACTIONr_mcbond_it1.991.7011909
X-RAY DIFFRACTIONr_mcbond_other1.9891.7011909
X-RAY DIFFRACTIONr_mcangle_it2.9783.0472395
X-RAY DIFFRACTIONr_mcangle_other2.9773.0482396
X-RAY DIFFRACTIONr_scbond_it3.0392.0071954
X-RAY DIFFRACTIONr_scbond_other3.0222.0061951
X-RAY DIFFRACTIONr_scangle_it4.5813.5142840
X-RAY DIFFRACTIONr_scangle_other4.5553.5112835
X-RAY DIFFRACTIONr_lrange_it5.92119.5964467
X-RAY DIFFRACTIONr_lrange_other5.9219.6014468
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
1.577-1.6180.2412170.22844660.22949760.9620.96194.11170.205
1.618-1.6620.2342550.20844660.2148410.9570.96797.52120.183
1.662-1.710.2382400.19944280.20147630.9610.9798.00550.171
1.71-1.7620.2532190.18342810.18645830.9580.97598.1890.156
1.762-1.820.1962070.16842250.1744930.9750.98198.64230.142
1.82-1.8840.1661950.15140990.15143360.9820.98599.03140.127
1.884-1.9540.1871760.15639830.15741810.9770.98499.47380.133
1.954-2.0340.1992240.15437660.15740110.9730.98599.47640.135
2.034-2.1240.191980.15336410.15538630.9780.98699.37870.138
2.124-2.2270.1761940.14535080.14737310.9820.98799.22270.13
2.227-2.3470.1721800.13733370.13935280.9820.98899.68820.125
2.347-2.4880.1751520.1431570.14233190.980.98899.69870.13
2.488-2.6590.2021600.15829960.1631620.9760.98599.81020.147
2.659-2.870.1941560.15628100.15829700.9780.98599.86530.149
2.87-3.1420.2031410.17225680.17427130.9740.98199.85260.171
3.142-3.5080.21220.16423810.16525030.9760.9841000.167
3.508-4.0420.1661170.14720920.14822090.9860.9881000.158
4.042-4.930.1561040.14318060.14419140.9860.98899.7910.16
4.93-6.8860.258730.18914180.19214930.9720.98299.8660.213
6.886-31.1820.214370.1848720.1859300.9780.97997.74190.212

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