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- PDB-4og7: Human menin with bound inhibitor MIV-7 -

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Basic information

Entry
Database: PDB / ID: 4og7
TitleHuman menin with bound inhibitor MIV-7
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 / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex / negative regulation of telomerase activity / 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 / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex / negative regulation of telomerase activity / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / MLL1 complex / cleavage furrow / negative regulation of cell cycle / RHO GTPases activate IQGAPs / negative regulation of osteoblast differentiation / four-way junction DNA binding / response to UV / transcription initiation-coupled chromatin remodeling / transcription repressor complex / negative regulation of protein phosphorylation / Deactivation of the beta-catenin transactivating complex / Post-translational protein phosphorylation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / negative regulation of DNA-binding transcription factor activity / nuclear matrix / phosphoprotein binding / 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-2SE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Menin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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)55,84510
Polymers54,6001
Non-polymers1,2459
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.040, 79.737, 124.801
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, 177 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2SE / 4-(3-{4-[(S)-cyclopentyl(hydroxy)pyridin-2-ylmethyl]piperidin-1-yl}propoxy)benzenesulfonamide


Mass: 473.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N3O4S
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
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: Dec 8, 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: 2.08→39.08 Å / Num. all: 189357 / Num. obs: 28805 / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 19.64

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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
Resolution: 2.08→39.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.418 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22177 1457 5.1 %RANDOM
Rwork0.17233 ---
obs0.17487 27206 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.08→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 78 168 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193821
X-RAY DIFFRACTIONr_bond_other_d0.0040.023644
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9785176
X-RAY DIFFRACTIONr_angle_other_deg1.0723.0078350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89223.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4581525
X-RAY DIFFRACTIONr_chiral_restr0.110.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214273
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_it1.7141.9921873
X-RAY DIFFRACTIONr_mcbond_other1.7141.9921874
X-RAY DIFFRACTIONr_mcangle_it2.6112.9752337
X-RAY DIFFRACTIONr_mcangle_other2.6112.9752337
X-RAY DIFFRACTIONr_scbond_it2.6132.2921948
X-RAY DIFFRACTIONr_scbond_other2.6132.2941949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7963.312840
X-RAY DIFFRACTIONr_long_range_B_refined5.97416.6234524
X-RAY DIFFRACTIONr_long_range_B_other5.93816.4664483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 94 -
Rwork0.223 1726 -
obs--86.34 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.12981.2510.91962.9672-0.24764.0249-0.0525-0.097-0.3356-0.0189-0.042-0.19580.42590.28240.09450.0920.0472-0.03130.16060.0540.16-5.76-10.121-0.065
21.76810.88120.38351.27570.16081.97930.0791-0.25510.01340.0843-0.04130.07520.1618-0.0081-0.03780.0857-0.0114-0.03220.19430.03170.102-16.636-5.6433.789
31.94070.7251.04833.01462.26165.7317-0.0161-0.20310.204-0.0121-0.03150.07650.0563-0.37170.04760.00350.01110.00140.17070.02570.1027-29.623-1.552-7.22
41.1755-0.34130.29180.9923-0.36021.43470.0625-0.1063-0.0160.02290.01410.05240.1509-0.0883-0.07660.0684-0.0311-0.00720.17460.01380.1294-21.728-0.276-9.857
52.1061-0.26050.62541.3374-1.12772.1858-0.0185-0.07740.0912-0.0620.06280.15120.0082-0.1616-0.04430.10020.0008-0.01110.178-0.0110.1485-21.1364.425-19.93
62.06950.3377-0.11481.1099-0.32112.00080.0737-0.20410.07780.116-0.1246-0.1251-0.02120.22240.05080.0205-0.0073-0.02640.16020.02140.1222-2.1827.097-5.922
70.29450.1744-0.02671.4173-0.32040.53210.0122-0.01570.0185-0.0223-0.0661-0.0782-0.02640.07420.05390.0181-0.0083-0.00480.13310.01550.1105-7.20223.335-21.122
83.73811.2524-2.71362.5689-1.26373.70090.02010.01460.0546-0.02450.00510.051-0.1934-0.0005-0.02520.08070.0228-0.02910.18080.02070.1466-10.10236.423-26.987
94.2096-1.58830.16336.60340.17171.147-0.12450.17210.22820.08150.0457-0.43640.01180.19490.07880.06410.002-0.06210.12060.02560.1147-12.56836.504-33.656
1036.2132-32.996211.632330.066-10.60013.7582-0.4478-0.9045-0.65690.36970.79380.6035-0.1163-0.3063-0.3460.423-0.0676-0.00970.25440.03630.6084-28.79243.728-29.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 37
2X-RAY DIFFRACTION2A38 - 109
3X-RAY DIFFRACTION3A110 - 136
4X-RAY DIFFRACTION4A137 - 202
5X-RAY DIFFRACTION5A203 - 238
6X-RAY DIFFRACTION6A239 - 295
7X-RAY DIFFRACTION7A296 - 428
8X-RAY DIFFRACTION8A429 - 460
9X-RAY DIFFRACTION9A461 - 580
10X-RAY DIFFRACTION10A581 - 588

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