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- PDB-9c4w: Menin mutant - G331R -

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Basic information

Entry
Database: PDB / ID: 9c4w
TitleMenin mutant - G331R
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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)55,42910
Polymers54,6701
Non-polymers7599
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.714, 80.012, 124.62
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: 54670.367 Da / Num. of mol.: 1 / Mutation: G331R
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.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.398→67.33 Å / Num. obs: 96452 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.7
Reflection shellResolution: 1.398→1.47 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13763 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOLREP11.0 / 22.07.2010/phasing
XDSdata reduction
Aimless0.7.15data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.398→67.329 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.89 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1812 4914 5.099 %
Rwork0.1576 91457 -
all0.159 --
obs-96371 99.361 %
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: 18.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.379 Å20 Å2-0 Å2
2--0.424 Å20 Å2
3----0.803 Å2
Refinement stepCycle: LAST / Resolution: 1.398→67.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 47 509 4220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163775
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.8315468
X-RAY DIFFRACTIONr_angle_other_deg0.6691.7488669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.786531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67110663
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.57210184
X-RAY DIFFRACTIONr_chiral_restr0.1020.2600
X-RAY DIFFRACTIONr_chiral_restr_other0.0010.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
X-RAY DIFFRACTIONr_nbd_refined0.2390.2847
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23374
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21989
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2305
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3830.213
X-RAY DIFFRACTIONr_nbd_other0.2390.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.222
X-RAY DIFFRACTIONr_mcbond_it1.7721.5681989
X-RAY DIFFRACTIONr_mcbond_other1.7721.5681989
X-RAY DIFFRACTIONr_mcangle_it2.6522.812523
X-RAY DIFFRACTIONr_mcangle_other2.6522.8112524
X-RAY DIFFRACTIONr_scbond_it2.991.8662028
X-RAY DIFFRACTIONr_scbond_other2.9891.8682029
X-RAY DIFFRACTIONr_scangle_it4.5433.2642945
X-RAY DIFFRACTIONr_scangle_other4.5433.2652946
X-RAY DIFFRACTIONr_lrange_it5.65618.0624733
X-RAY DIFFRACTIONr_lrange_other5.55716.9364615
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
1.398-1.4350.2223270.22165980.22170550.9660.96998.15730.214
1.435-1.4740.2013520.20364720.20369130.9740.97498.71260.192
1.474-1.5170.2083630.18263040.18367300.9740.97999.06390.169
1.517-1.5630.1833510.17261220.17265310.9790.98299.11190.157
1.563-1.6150.1923120.16459810.16563420.9770.98399.22740.147
1.615-1.6710.1763110.15557800.15661400.9810.98599.2020.139
1.671-1.7340.1813060.15155930.15359440.980.98599.24290.135
1.734-1.8050.182830.14953740.15157020.9780.98699.21080.134
1.805-1.8850.1823030.15151490.15254700.980.98699.67090.138
1.885-1.9770.1862630.15649620.15752370.980.98699.77090.145
1.977-2.0840.192580.15447710.15650370.980.98799.84120.146
2.084-2.210.182300.15344950.15547300.980.98899.89430.147
2.21-2.3630.1622190.1442480.14144720.9850.98999.88820.137
2.363-2.5520.1672170.13939480.1441660.9840.98899.9760.14
2.552-2.7950.1821990.15136420.15338410.980.9861000.156
2.795-3.1240.2021680.16333600.16535280.9770.9831000.174
3.124-3.6060.1791580.1529520.15231100.980.9871000.167
3.606-4.4130.1551440.13725180.13826620.9860.9881000.166
4.413-6.2280.179940.17920110.17921050.9860.9861000.218
6.228-67.3290.209560.19811770.19812390.9730.97899.51570.264

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