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- PDB-3u85: Crystal structure of human menin in complex with MLL1 -

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Basic information

Entry
Database: PDB / ID: 3u85
TitleCrystal structure of human menin in complex with MLL1
Components
  • Histone-lysine N-methyltransferase 2A
  • Menin
KeywordsTRANSCRIPTION / menin / MEN1 / MLL / JunD / LEDGF / TPR / epigenetics / cancer
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / Y-form DNA binding / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of cyclin-dependent protein serine/threonine kinase activity ...protein-cysteine methyltransferase activity / Y-form DNA binding / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / regulation of short-term neuronal synaptic plasticity / MLL1/2 complex / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / osteoblast development / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / minor groove of adenine-thymine-rich DNA binding / R-SMAD binding / membrane depolarization / cleavage furrow / MLL1 complex / negative regulation of cell cycle / RHO GTPases activate IQGAPs / negative regulation of osteoblast differentiation / response to UV / four-way junction DNA binding / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / transcription repressor complex / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / 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 / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / negative regulation of DNA-binding transcription factor activity / PKMTs methylate histone lysines / nuclear matrix / Transcriptional regulation of granulopoiesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / protein-containing complex assembly / 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 / apoptotic process / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Menin / Menin / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus ...Menin / Menin / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Menin / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref.db_code / _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
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

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Assembly

Deposited unit
A: Menin
B: Histone-lysine N-methyltransferase 2A


Theoretical massNumber of molelcules
Total (without water)63,2102
Polymers63,2102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area22500 Å2
MethodPISA
2
A: Menin
B: Histone-lysine N-methyltransferase 2A

A: Menin
B: Histone-lysine N-methyltransferase 2A


Theoretical massNumber of molelcules
Total (without water)126,4194
Polymers126,4194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5550 Å2
ΔGint-25 kcal/mol
Surface area42380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.205, 141.205, 93.550
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 Histone-lysine N-methyltransferase 2A / Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed- ...Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed-lineage leukemia / Myeloid/lymphoid or mixed-lineage leukemia protein 1 / Trithorax-like protein / Zinc finger protein HRX


Mass: 2148.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03164, histone-lysine N-methyltransferase

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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: 3.69 Å3/Da / Density % sol: 66.65 %
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: 0.97941 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: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 18712 / % possible obs: 94.6 % / Redundancy: 23.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.367 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.1120.40.33414600.913175.5
3.11-3.2320.70.24715821.037181.3
3.23-3.38210.20117851.105192.5
3.38-3.5622.70.16318961.188197.7
3.56-3.7824.70.13219461.332199.7
3.78-4.0726.10.119541.3131100
4.07-4.48260.08619731.4591100
4.48-5.1325.80.08319781.7251100
5.13-6.4625.50.06920281.5741100
6.46-10022.30.0621101.635198.2

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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: 3→33.282 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7014 / SU ML: 0.3 / σ(F): 1.2 / Phase error: 33.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1808 9.81 %
Rwork0.2202 --
obs0.224 18424 94.62 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.033 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 190 Å2 / Biso mean: 111.0117 Å2 / Biso min: 64.38 Å2
Baniso -1Baniso -2Baniso -3
1--43.2274 Å2-0 Å20 Å2
2---43.2274 Å2-0 Å2
3---95.0929 Å2
Refinement stepCycle: LAST / Resolution: 3→33.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 0 0 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043988
X-RAY DIFFRACTIONf_angle_d0.8095416
X-RAY DIFFRACTIONf_chiral_restr0.052601
X-RAY DIFFRACTIONf_plane_restr0.004698
X-RAY DIFFRACTIONf_dihedral_angle_d15.3751458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.08120.4114910.34411029112075
3.0812-3.17180.34831160.31831017113378
3.1718-3.2740.33741430.30331149129288
3.274-3.3910.34311350.30041262139795
3.391-3.52660.32411160.27251307142397
3.5266-3.68690.31991250.23731340146599
3.6869-3.8810.2541510.21821315146699
3.881-4.12370.24961470.20111328147599
4.1237-4.44150.22651510.186413521503100
4.4415-4.88720.21921600.185613371497100
4.8872-5.59150.2121530.190213441497100
5.5915-7.03370.23791580.212613851543100
7.0337-33.28440.2511620.20561451161399

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