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- PDB-9c4y: Menin mutant - T349M -

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Basic information

Entry
Database: PDB / ID: 9c4y
TitleMenin mutant - T349M
ComponentsMenin
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


Y-form DNA binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / MLL1/2 complex / negative regulation of JNK cascade / osteoblast development / T-helper 2 cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding ...Y-form DNA binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / MLL1/2 complex / negative regulation of JNK cascade / osteoblast development / T-helper 2 cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / cleavage furrow / MLL1 complex / negative regulation of cell cycle / negative regulation of protein phosphorylation / 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 / negative regulation of DNA-binding transcription factor activity / phosphoprotein binding / Post-translational protein phosphorylation / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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: 1.309 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2277
Polymers54,6001
Non-polymers6276
Water10,593588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.024, 80.268, 124.941
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 , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 594 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.36 %
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: 1.309→50 Å / Num. obs: 118901 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 30.02
Reflection shellResolution: 1.309→1.33 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.707 / Num. unique obs: 5800 / % possible all: 98.3

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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: 1.309→28.916 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.721 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1829 5836 4.912 %
Rwork0.1617 112984 -
all0.163 --
obs-118820 99.607 %
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: 14.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.057 Å2-0 Å20 Å2
2---0.159 Å2-0 Å2
3---0.216 Å2
Refinement stepCycle: LAST / Resolution: 1.309→28.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 40 590 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123866
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163650
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.8265242
X-RAY DIFFRACTIONr_angle_other_deg0.6591.7428394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.497525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42410639
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.68210171
X-RAY DIFFRACTIONr_chiral_restr0.10.2582
X-RAY DIFFRACTIONr_chiral_restr_other00.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined0.2340.2790
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23291
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21916
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2326
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3270.212
X-RAY DIFFRACTIONr_nbd_other0.2080.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.227
X-RAY DIFFRACTIONr_mcbond_it1.5441.2111924
X-RAY DIFFRACTIONr_mcbond_other1.5431.2111924
X-RAY DIFFRACTIONr_mcangle_it2.3412.1742419
X-RAY DIFFRACTIONr_mcangle_other2.3412.1742420
X-RAY DIFFRACTIONr_scbond_it2.6091.4511942
X-RAY DIFFRACTIONr_scbond_other2.6091.4521943
X-RAY DIFFRACTIONr_scangle_it3.952.5272823
X-RAY DIFFRACTIONr_scangle_other3.9492.5282824
X-RAY DIFFRACTIONr_lrange_it5.29614.7074544
X-RAY DIFFRACTIONr_lrange_other5.29614.7094545
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
1.309-1.3430.254020.24679770.24687320.9620.96595.95740.218
1.343-1.380.2344390.21180190.21384840.9660.97299.69350.185
1.38-1.420.2263950.278440.20282610.9680.97599.73370.174
1.42-1.4630.1983860.1876160.18180120.9760.97999.87520.154
1.463-1.5110.1884030.17273850.17377950.9760.98199.91020.148
1.511-1.5640.1893610.16171850.16275510.9780.98399.93380.14
1.564-1.6230.193800.15669030.15872850.9780.98599.97250.137
1.623-1.6890.1753260.15367020.15570280.9810.9851000.136
1.689-1.7640.1943400.15563920.15767320.9770.9851000.139
1.764-1.850.1852970.15161530.15364500.9780.9861000.138
1.85-1.9490.1892970.15658670.15861640.9780.9851000.146
1.949-2.0670.172820.15455360.15558180.9830.9861000.148
2.067-2.2090.1692520.14652370.14754890.9820.9871000.145
2.209-2.3850.1682490.13948750.1451240.9820.9881000.139
2.385-2.610.1722350.14845390.14947740.9810.9861000.153
2.61-2.9160.1792120.15740840.15842960.9790.9851000.166
2.916-3.3610.172120.16436290.16538410.9810.9841000.179
3.361-4.1030.1671510.14831320.14932830.9830.9871000.169
4.103-5.7440.1891490.16324330.16425850.9840.98799.88390.198
5.744-28.9160.183680.21114760.2115670.9830.97798.53220.265

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