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- PDB-4og6: Human menin with bound inhibitor MIV-4 -

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Basic information

Entry
Database: PDB / ID: 4og6
TitleHuman menin with bound inhibitor MIV-4
ComponentsMenin
KeywordsPROTEIN BINDING/INHIBITOR / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


Y-form DNA binding / : / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / T-helper 2 cell differentiation / MLL1/2 complex / 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 cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / T-helper 2 cell differentiation / MLL1/2 complex / 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 / 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 / negative regulation of protein phosphorylation / response to gamma radiation / Deactivation of the beta-catenin transactivating complex / phosphoprotein binding / Post-translational protein phosphorylation / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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 / cytosol / cytoplasm
Similarity search - Function
Chem-2S9 / DI(HYDROXYETHYL)ETHER / Menin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)55,95811
Polymers54,6001
Non-polymers1,35810
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.568, 79.865, 124.464
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: 54600.246 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, 473 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2S9 / 4-(3-{4-[(R)-cyclopentyl(3-fluorophenyl)hydroxymethyl]piperidin-1-yl}propoxy)benzonitrile


Mass: 436.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33FN2O2
#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.: 3 / 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.: 463 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data ...Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.49→38.02 Å / Num. all: 368758 / Num. obs: 74065 / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.38

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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
Starting model: pdb entry 4GPQ

4gpq


Resolution: 1.49→38.02 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.37 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18819 3701 5 %RANDOM
Rwork0.16062 ---
obs0.16202 70287 92.71 %-
all-74065 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2---0.26 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.49→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 84 463 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193930
X-RAY DIFFRACTIONr_bond_other_d0.0040.023737
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9795326
X-RAY DIFFRACTIONr_angle_other_deg1.0543.0088586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59323.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06315644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1341526
X-RAY DIFFRACTIONr_chiral_restr0.1220.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02912
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_it2.5491.3891916
X-RAY DIFFRACTIONr_mcbond_other2.5471.3871915
X-RAY DIFFRACTIONr_mcangle_it3.3112.1662402
X-RAY DIFFRACTIONr_mcangle_other3.3112.1682403
X-RAY DIFFRACTIONr_scbond_it4.0342.3912014
X-RAY DIFFRACTIONr_scbond_other4.0312.3912014
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.283.2972924
X-RAY DIFFRACTIONr_long_range_B_refined8.0937.3274991
X-RAY DIFFRACTIONr_long_range_B_other8.0927.3344992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.491→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 254 -
Rwork0.219 4507 -
obs--81.78 %
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)
11.5410.6958-0.39521.9971-0.88631.9004-0.0658-0.0514-0.2139-0.1390.0061-0.1110.3540.17050.05960.15790.0392-0.00780.19910.01470.1153-4.423-10.4781.181
21.37720.48810.28010.81610.02531.51040.057-0.17-0.00140.0163-0.046-0.0150.1409-0.0218-0.0110.1051-0.0004-0.01120.21480.00520.0733-12.768-3.5116.066
32.35840.7070.35370.2949-0.38023.5063-0.006-0.1221-0.2099-0.0388-0.0265-0.04020.4491-0.20980.03250.1993-0.04890.01160.23860.01670.1277-30.334-10.946-11.334
48.220511.07692.068820.8304-2.43465.1437-0.137-0.28830.78250.3633-0.04761.0693-0.4934-0.37840.18460.13620.069-0.00760.2352-0.05380.1977-28.0768.6561.463
50.539-0.10040.34290.3555-0.09641.3460.0412-0.0515-0.0002-0.01360.01750.0630.11-0.1281-0.05870.0898-0.0277-0.00850.18790.00290.0756-22.9741.873-13.662
60.392-0.04330.26940.5367-0.51321.1619-0.0107-0.00690.04620.0155-0.0743-0.0974-0.00580.13990.0850.0756-0.0001-0.00130.20070.00570.0922-3.798.847-11.884
70.54380.37490.02011.25970.09230.88270.009-0.0627-0.00030.0114-0.04380.0059-0.00420.00040.03480.0690.0084-0.00350.18680.00950.0703-10.80428.64-21.97
811.92491.7048-7.8570.2812-0.80258.08220.2988-0.13380.6149-0.00180.04390.1042-0.67570.6069-0.34270.1448-0.05910.00780.31740.02480.1052-4.23440.902-23.51
95.28093.4721.53442.9071.03420.7653-0.20890.34-0.2273-0.33910.2449-0.2331-0.21020.145-0.0360.1457-0.00780.01310.2141-0.00680.0831-6.80533.834-35.941
103.5406-2.12231.71032.2686-0.25891.4369-0.1757-0.07550.27950.30580.1061-0.22530.0292-0.01580.06960.18420.0348-0.04610.187-0.00670.1218-18.51742.526-30.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 30
2X-RAY DIFFRACTION2A31 - 97
3X-RAY DIFFRACTION3A98 - 127
4X-RAY DIFFRACTION4A128 - 137
5X-RAY DIFFRACTION5A138 - 227
6X-RAY DIFFRACTION6A228 - 333
7X-RAY DIFFRACTION7A334 - 443
8X-RAY DIFFRACTION8A444 - 448
9X-RAY DIFFRACTION9A449 - 561
10X-RAY DIFFRACTION10A562 - 588

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