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- PDB-3u86: Crystal structure of human menin in complex with JunD -

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Basic information

Entry
Database: PDB / ID: 3u86
TitleCrystal structure of human menin in complex with JunD
Components
  • Menin
  • Transcription factor jun-D
KeywordsTRANSCRIPTION / menin / MEN1 / MLL / JunD / LEDGF / TPR / epigenetics / cancer
Function / homology
Function and homology information


transcription factor AP-1 complex / Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / NGF-stimulated transcription / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex ...transcription factor AP-1 complex / Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / NGF-stimulated transcription / 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 / positive regulation of osteoblast differentiation / four-way junction DNA binding / response to UV / transcription initiation-coupled chromatin remodeling / cellular response to calcium ion / transcription repressor complex / negative regulation of protein phosphorylation / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / 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 / RNA polymerase II transcription regulator complex / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / sequence-specific double-stranded DNA binding / protein-macromolecule adaptor activity / gene expression / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA 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 / enzyme binding / 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
Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Menin / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Menin / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Menin / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Menin / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
Menin / Transcription factor JunD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.843 Å
AuthorsHuang, J. / Wan, B. / Lei, M.
CitationJournal: Nature / Year: 2012
Title: The same pocket in menin binds both MLL and JUND but has opposite effects on transcription.
Authors: Huang, J. / Gurung, B. / Wan, B. / Matkar, S. / Veniaminova, N.A. / Wan, K. / Merchant, J.L. / Hua, X. / Lei, M.
History
DepositionOct 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_entry_details ...entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Menin
B: Transcription factor jun-D


Theoretical massNumber of molelcules
Total (without water)62,5882
Polymers62,5882
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.647, 140.647, 93.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Menin


Mass: 61061.234 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) / Strain (production host): BL21(DE3) / References: UniProt: O00255
#2: Protein/peptide Transcription factor jun-D


Mass: 1526.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUND / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17535*PLUS

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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: 3.68 Å3/Da / Density % sol: 66.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98019 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98019 Å / Relative weight: 1
ReflectionResolution: 2.843→100 Å / Num. obs: 21430 / % possible obs: 95 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.1 / Χ2: 1.215 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.959.50.44616470.771175.1
2.95-3.07100.3618710.867184.1
3.07-3.2110.20.26820670.936193.4
3.21-3.3811.30.2121821.051198.4
3.38-3.5912.20.16422151.16199.7
3.59-3.8712.60.12422331.3371100
3.87-4.2612.60.09722451.3521100
4.26-4.8712.50.08422661.5151100
4.87-6.1412.30.07522921.3621100
6.14-100110.06324121.387198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.843→33.984 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7372 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 2148 10.06 %
Rwork0.2168 --
obs0.2195 21352 94.86 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.962 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 176.87 Å2 / Biso mean: 95.4543 Å2 / Biso min: 62.9 Å2
Baniso -1Baniso -2Baniso -3
1--37.5594 Å2-0 Å20 Å2
2---37.5594 Å2-0 Å2
3---75.1188 Å2
Refinement stepCycle: LAST / Resolution: 2.843→33.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 0 0 3902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073994
X-RAY DIFFRACTIONf_angle_d1.0325424
X-RAY DIFFRACTIONf_chiral_restr0.073605
X-RAY DIFFRACTIONf_plane_restr0.004699
X-RAY DIFFRACTIONf_dihedral_angle_d15.7221462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.843-2.90960.2942980.29721002110074
2.9096-2.98230.32331200.27891006112677
2.9823-3.06290.34581320.30811141127387
3.0629-3.15290.36441460.29131211135792
3.1529-3.25460.30211540.26421253140796
3.2546-3.37080.31271650.25091308147399
3.3708-3.50570.32261420.23071311145399
3.5057-3.6650.26321420.215213431485100
3.665-3.8580.20211540.204413421496100
3.858-4.09940.23051430.197213411484100
4.0994-4.41520.23991440.188913591503100
4.4152-4.85840.20441470.183113641511100
4.8584-5.55880.21091610.203413541515100
5.5588-6.99350.23021540.22613911545100
6.9935-33.98680.21321460.20081478162499

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