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- PDB-4og3: Human menin with bound inhibitor MIV-3R -

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Basic information

Entry
Database: PDB / ID: 4og3
TitleHuman menin with bound inhibitor MIV-3R
ComponentsMenin
KeywordsPROTEIN BINDING/INHIBITOR / Protein Binding / PROTEIN BINDING-INHIBITOR complex
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
Chem-2S6 / DI(HYDROXYETHYL)ETHER / Menin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHe, S. / Senter, T.J. / Pollock, J.W. / Han, C. / Upadhyay, S.K. / Purohit, T. / Gogliotti, R.D. / Lindsley, C.W. / Cierpicki, T. / Stauffer, S.R. / Grembecka, J.
CitationJournal: J.Med.Chem. / Year: 2014
Title: High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction.
Authors: He, S. / Senter, T.J. / Pollock, J. / Han, C. / Upadhyay, S.K. / Purohit, T. / Gogliotti, R.D. / Lindsley, C.W. / Cierpicki, T. / Stauffer, S.R. / Grembecka, J.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,00010
Polymers53,7661
Non-polymers1,2349
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.868, 80.256, 124.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 53766.367 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 (E. coli) / References: UniProt: O00255

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Non-polymers , 6 types, 331 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2S6 / 4-(3-{4-[(R)-cyclopentyl(hydroxy)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile


Mass: 418.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N2O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE HUMAN MENIN ISOFORM 2

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals ...Details: 0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.01→39.581 Å / Num. all: 242461 / Num. obs: 33475 / % possible obs: 100 % / Observed criterion σ(F): 1 / Rsym value: 0.145 / Net I/σ(I): 16.89

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→39.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.805 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20847 1691 5.1 %RANDOM
Rwork0.15543 ---
obs0.15813 31704 99.85 %-
all-33475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 79 322 4027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193806
X-RAY DIFFRACTIONr_bond_other_d0.0040.023609
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9765155
X-RAY DIFFRACTIONr_angle_other_deg1.1033.0088273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89423.69168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12815608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9111524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5431.6081874
X-RAY DIFFRACTIONr_mcbond_other1.5431.6071873
X-RAY DIFFRACTIONr_mcangle_it2.3362.3992341
X-RAY DIFFRACTIONr_mcangle_other2.3362.3992342
X-RAY DIFFRACTIONr_scbond_it2.1661.8841932
X-RAY DIFFRACTIONr_scbond_other2.1661.8861933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2512.7042815
X-RAY DIFFRACTIONr_long_range_B_refined614.1564678
X-RAY DIFFRACTIONr_long_range_B_other5.99914.1684679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 106 -
Rwork0.184 2278 -
obs--98.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6149-0.2472-0.60091.9888-0.62452.5665-0.0542-0.101-0.2710.0485-0.0393-0.07160.30060.10560.09350.07190.0157-0.02420.0230.02240.0811-4.226-9.6482.228
21.74890.82760.55982.04910.5892.06990.0459-0.1708-0.0521-0.00530.026-0.01240.07560.057-0.07190.0590.0019-0.0080.06570.01090.0376-12.312-3.8565.438
32.61410.24570.36251.29670.09223.46980.0088-0.039-0.2887-0.1218-0.01630.00380.2172-0.07130.00740.0811-0.03080.00450.04470.02140.0791-30.356-9.79-9.984
423.9186-1.4688-2.372222.6766-1.94562.309-0.0061-0.05121.17970.5443-0.17131.6706-0.1705-0.02340.17740.08140.01370.01130.0597-0.04260.3068-27.8910.7921.184
50.69-0.03540.15670.4595-0.18211.39580.0263-0.00770.0454-0.01520.00420.0850.032-0.1411-0.03060.0563-0.0262-0.0110.0375-0.00010.068-23.0022.055-13.805
61.6250.14920.1470.7471-0.36491.36840.0281-0.04560.10170.0157-0.0923-0.0405-0.03360.06390.06420.05840.0029-0.00320.02090.00630.0729-5.1065.21-7.323
70.7496-0.28520.36841.386-0.46721.2702-0.0097-0.01310.07280.0162-0.0513-0.0919-0.01580.0870.0610.0418-0.00580.01210.03220.00340.0847-4.95516.154-20.044
84.933.33880.72673.89360.33831.07190.0687-0.2450.04290.1589-0.12770.0396-0.00350.02090.0590.05230.0121-0.00230.05080.00030.022-9.48630.389-15.774
92.48131.2369-0.35231.8495-0.06171.8185-0.0419-0.0015-0.0791-0.09480.0312-0.0212-0.0822-0.01830.01070.05820.019-0.01430.02360.0170.0585-10.14733.022-27.339
102.8086-1.41840.67854.64610.37050.4517-0.1080.07840.22990.09470.04-0.2255-0.1332-0.02160.0680.09740.0304-0.0480.0270.00330.0506-15.67338.028-32.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 28
2X-RAY DIFFRACTION2A29 - 96
3X-RAY DIFFRACTION3A97 - 130
4X-RAY DIFFRACTION4A131 - 137
5X-RAY DIFFRACTION5A138 - 228
6X-RAY DIFFRACTION6A229 - 289
7X-RAY DIFFRACTION7A290 - 355
8X-RAY DIFFRACTION8A356 - 401
9X-RAY DIFFRACTION9A402 - 548
10X-RAY DIFFRACTION10A549 - 586

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