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- PDB-3u84: Crystal Structure of Human Menin -

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Basic information

Entry
Database: PDB / ID: 3u84
TitleCrystal Structure of Human Menin
ComponentsMenin
KeywordsTRANSCRIPTION / menin / MEN1 / MLL / JunD / LEDGF / TPR / transglutaminase-like / epigenetics / cancer
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 / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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.pdbx_align_begin / _struct_ref.pdbx_db_isoform ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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: Menin


Theoretical massNumber of molelcules
Total (without water)122,1222
Polymers122,1222
Non-polymers00
Water90150
1
A: Menin


Theoretical massNumber of molelcules
Total (without water)61,0611
Polymers61,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Menin


Theoretical massNumber of molelcules
Total (without water)61,0611
Polymers61,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Menin

B: Menin


Theoretical massNumber of molelcules
Total (without water)122,1222
Polymers122,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,-y-1,z-1/21
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area42910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.891, 139.891, 54.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Menin


Mass: 61061.234 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M sodium acetate, pH 6.5, 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: 1.07819 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07819 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 36832 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.096 / Χ2: 1.397 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.595.50.46536791.0161100
2.59-2.696.60.41536441.0411100
2.69-2.8270.31336211.0881100
2.82-2.967.10.23136421.161100
2.96-3.157.20.17336691.2651100
3.15-3.397.40.1336851.4491100
3.39-3.737.50.09236581.5721100
3.73-4.277.50.07536801.7351100
4.27-5.397.40.07137491.8961100
5.39-1007.20.04938051.525199.7

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.941 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8302 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 3663 9.99 %
Rwork0.1975 --
obs0.2012 36667 99.92 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.25 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso max: 140.01 Å2 / Biso mean: 49.4121 Å2 / Biso min: 2.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.1376 Å20 Å2-0 Å2
2--2.1376 Å20 Å2
3----4.2752 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7703 0 0 50 7753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037877
X-RAY DIFFRACTIONf_angle_d0.71710691
X-RAY DIFFRACTIONf_chiral_restr0.0481199
X-RAY DIFFRACTIONf_plane_restr0.0031372
X-RAY DIFFRACTIONf_dihedral_angle_d14.9982868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.53290.31991360.262712371373100
2.5329-2.56760.30831420.254412551397100
2.5676-2.60430.34461300.260312711401100
2.6043-2.64310.32971470.271112341381100
2.6431-2.68440.29851530.261612631416100
2.6844-2.72840.31281340.269612551389100
2.7284-2.77550.30711460.250712481394100
2.7755-2.82590.28851640.257912391403100
2.8259-2.88030.32991560.250812361392100
2.8803-2.9390.34141210.247312951416100
2.939-3.00290.27861390.236712831422100
3.0029-3.07280.2861590.231612081367100
3.0728-3.14960.26581260.221812821408100
3.1496-3.23470.25461110.209413011412100
3.2347-3.32990.27241730.215812481421100
3.3299-3.43730.24871420.202912411383100
3.4373-3.56010.23841530.196312721425100
3.5601-3.70250.24211360.187712671403100
3.7025-3.87090.19811430.168612971440100
3.8709-4.07480.17151340.161712511385100
4.0748-4.32980.17821380.148512771415100
4.3298-4.66370.15461250.144813211446100
4.6637-5.13230.1851310.156612841415100
5.1323-5.8730.20231400.193312961436100
5.873-7.39230.24771320.193613131445100
7.3923-40.94690.1851520.18061330148299

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