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- PDB-7oa9: Crystal structure of Human Menin in complex with Fragment 21 -

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Basic information

Entry
Database: PDB / ID: 7oa9
TitleCrystal structure of Human Menin in complex with Fragment 21
ComponentsIsoform 2 of Menin
KeywordsONCOPROTEIN
Function / homology
Function and homology information


Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway ...Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / 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 / RHO GTPases activate IQGAPs / negative regulation of osteoblast differentiation / response to UV / four-way junction DNA binding / transcription initiation-coupled chromatin remodeling / transcription repressor complex / negative regulation of protein phosphorylation / Deactivation of the beta-catenin transactivating complex / response to gamma radiation / phosphoprotein binding / Post-translational protein phosphorylation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / negative regulation of DNA-binding transcription factor activity / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / protein-macromolecule adaptor activity / double-stranded DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / negative regulation of cell population proliferation / endoplasmic reticulum lumen / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsGroves, M.R. / Gao, K.
CitationJournal: To Be Published
Title: Crystal structure of Human Menin in complex with Fragment 21
Authors: Groves, M.R. / Gao, K.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Menin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86110
Polymers56,0341
Non-polymers8289
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint19 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.399, 107.399, 107.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

21A-727-

HOH

31A-862-

HOH

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Components

#1: Protein Isoform 2 of Menin


Mass: 56033.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, SCG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00255
#2: Chemical ChemComp-V6K / (~{E})-2-cyano-3-(4-hydroxyphenyl)-~{N}-(2-morpholin-4-ylethyl)prop-2-enamide


Mass: 301.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 3350 14% Glycerol / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.098→49 Å / Num. obs: 37566 / % possible obs: 99.93 % / Redundancy: 17.6 % / Biso Wilson estimate: 36.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.09 / Net I/σ(I): 22
Reflection shellResolution: 2.098→2.173 Å / Redundancy: 12 % / Rmerge(I) obs: 0.582 / Num. unique obs: 3674 / CC1/2: 0.957 / CC star: 0.989 / Rrim(I) all: 0.599 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DDC

5ddc


Resolution: 2.098→48.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1780 4.74 %
Rwork0.1969 35770 -
obs0.1987 37550 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.27 Å2 / Biso mean: 46.261 Å2 / Biso min: 21.24 Å2
Refinement stepCycle: final / Resolution: 2.098→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 56 169 3819
Biso mean--49.97 44.91 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083720
X-RAY DIFFRACTIONf_angle_d0.8285022
X-RAY DIFFRACTIONf_chiral_restr0.051556
X-RAY DIFFRACTIONf_plane_restr0.005640
X-RAY DIFFRACTIONf_dihedral_angle_d11.9492210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15420.27231220.2294267599
2.1542-2.21760.24321410.22722693100
2.2176-2.28920.30551220.21952736100
2.2892-2.3710.26391150.21972724100
2.371-2.4660.27611620.2212684100
2.466-2.57820.26121430.21492729100
2.5782-2.71410.24591000.21212758100
2.7141-2.88410.25621230.21522730100
2.8841-3.10680.27111330.20242764100
3.1068-3.41930.22321470.1942738100
3.4193-3.91390.21431690.17942759100
3.9139-4.93040.20231430.17512817100
4.9304-70.2341600.19592963100

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