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- PDB-9c4z: Menin mutant - G331D -

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Basic information

Entry
Database: PDB / ID: 9c4z
TitleMenin mutant - G331D
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: 1.4 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 - G331D
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)55,3777
Polymers54,6281
Non-polymers7496
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.729, 79.937, 124.71
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: 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

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Non-polymers , 5 types, 512 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
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 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 96464 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 34
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.852 / Num. unique obs: 4763 / % possible all: 100

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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: 1.4→24.963 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.051 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.19 4811 4.991 %
Rwork0.1653 91574 -
all0.167 --
obs-96385 99.73 %
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: 18.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.777 Å20 Å20 Å2
2---0.283 Å20 Å2
3----0.494 Å2
Refinement stepCycle: LAST / Resolution: 1.4→24.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 47 506 4199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123907
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163661
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.8245312
X-RAY DIFFRACTIONr_angle_other_deg0.6871.7428423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.235524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19110637
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.36810175
X-RAY DIFFRACTIONr_chiral_restr0.1080.2590
X-RAY DIFFRACTIONr_chiral_restr_other00.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02913
X-RAY DIFFRACTIONr_nbd_refined0.2340.2785
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23275
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21929
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2318
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.212
X-RAY DIFFRACTIONr_nbd_other0.1650.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.218
X-RAY DIFFRACTIONr_mcbond_it1.8151.6451940
X-RAY DIFFRACTIONr_mcbond_other1.8151.6451940
X-RAY DIFFRACTIONr_mcangle_it2.6782.9512446
X-RAY DIFFRACTIONr_mcangle_other2.6772.9532447
X-RAY DIFFRACTIONr_scbond_it3.0621.9121967
X-RAY DIFFRACTIONr_scbond_other3.0611.9131968
X-RAY DIFFRACTIONr_scangle_it4.5823.3672866
X-RAY DIFFRACTIONr_scangle_other4.5813.3682867
X-RAY DIFFRACTIONr_lrange_it5.72518.5184573
X-RAY DIFFRACTIONr_lrange_other5.72618.5234574
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
1.4-1.4360.2783190.25765970.25870320.9430.95498.35040.234
1.436-1.4750.273760.22764770.2368530.9530.9651000.2
1.475-1.5180.223240.20463560.20566800.9670.9721000.177
1.518-1.5650.213310.18561650.18664960.9720.9771000.16
1.565-1.6160.2163470.17859730.1863200.9690.9791000.153
1.616-1.6720.2192990.17158030.17361020.9690.9811000.146
1.672-1.7350.2083140.16856060.1759200.9740.9821000.145
1.735-1.8050.1892580.16254110.16456690.9770.9831000.141
1.805-1.8850.22690.15951700.16154390.9730.9841000.142
1.885-1.9770.1832470.16349730.16452200.9780.9841000.15
1.977-2.0830.1932260.15947810.1650070.9760.9851000.15
2.083-2.2080.1852060.15845070.15947140.9780.98599.97880.152
2.208-2.3590.1742260.14442250.14544510.980.9871000.141
2.359-2.5470.1712070.14239520.14441600.9830.98799.9760.143
2.547-2.7870.1792170.15536210.15638400.9790.98599.94790.159
2.787-3.1110.1861990.16533080.16635110.9770.98399.88610.175
3.111-3.5830.1811430.1629440.16130960.980.98599.70930.176
3.583-4.3650.1731250.14225350.14426800.9830.98799.25370.165
4.365-6.0810.1721140.17820020.17821280.9850.98599.43610.208
6.081-24.9630.196640.2111680.20913060.9820.97794.33380.253

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