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- PDB-3u88: Crystal structure of human menin in complex with MLL1 and LEDGF -

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Basic information

Entry
Database: PDB / ID: 3u88
TitleCrystal structure of human menin in complex with MLL1 and LEDGF
Components
  • Histone-lysine N-methyltransferase 2A
  • Lens epithelium-derived growth factor
  • Menin
KeywordsTRANSCRIPTION / menin / MEN1 / MLL / JunD / LEDGF / TPR
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / Y-form DNA binding / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / 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 / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / 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 / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / MLL1/2 complex / definitive hemopoiesis / histone H3K4 methyltransferase activity / supercoiled DNA binding / osteoblast development / embryonic hemopoiesis / anterior/posterior pattern specification / exploration behavior / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / histone methyltransferase complex / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / minor groove of adenine-thymine-rich DNA binding / R-SMAD binding / cleavage furrow / membrane depolarization / MLL1 complex / negative regulation of cell cycle / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / heterochromatin / response to UV / negative regulation of fibroblast proliferation / four-way junction DNA binding / spleen development / homeostasis of number of cells within a tissue / cellular response to transforming growth factor beta stimulus / transcription repressor complex / nuclear periphery / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / negative regulation of protein phosphorylation / response to gamma radiation / Deactivation of the beta-catenin transactivating complex / phosphoprotein binding / Post-translational protein phosphorylation / lysine-acetylated histone binding / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / euchromatin / negative regulation of DNA-binding transcription factor activity / protein modification process / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-macromolecule adaptor activity / response to heat / fibroblast proliferation / double-stranded DNA binding / protein-containing complex assembly / DNA-binding transcription factor binding / methylation / response to oxidative stress / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / 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 / apoptotic process / 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 / RNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2390 / Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Menin / Menin / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2390 / Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / 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 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Transcription Elongation Factor S-II; Chain A / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain superfamily / SET domain profile. / SET domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / PHD-finger / Zinc finger PHD-type signature. / Helix non-globular / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Special / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0BR / CHOLIC ACID / L-CANAVANINE / GLYOXYLIC ACID / Menin / PC4 and SFRS1-interacting protein / 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 16, 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 / 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Menin
M: Histone-lysine N-methyltransferase 2A
C: Lens epithelium-derived growth factor
N: Histone-lysine N-methyltransferase 2A
D: Lens epithelium-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,94429
Polymers158,3806
Non-polymers3,56423
Water00
1
A: Menin
M: Histone-lysine N-methyltransferase 2A
C: Lens epithelium-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,31017
Polymers79,1903
Non-polymers2,12014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-36 kcal/mol
Surface area26520 Å2
MethodPISA
2
B: Menin
N: Histone-lysine N-methyltransferase 2A
D: Lens epithelium-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,63412
Polymers79,1903
Non-polymers1,4439
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-38 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.990, 187.990, 238.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 3 types, 6 molecules ABMNCD

#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: Protein 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: 7782.705 Da / Num. of mol.: 2
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
#3: Protein Lens epithelium-derived growth factor / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Transcriptional ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Transcriptional coactivator p75/p52


Mass: 10346.106 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75475

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Non-polymers , 5 types, 23 molecules

#4: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5
#5: Chemical
ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12N4O3
#6: Chemical ChemComp-0BR / (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol


Mass: 326.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N2O2
#7: Chemical
ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H2O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 277 K / pH: 7
Details: 1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 22.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.65 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.42 / σ(F): 1.33 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 5048 10.07 %
Rwork0.202 --
obs0.205 50106 99.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.05 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 77.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.3808 Å20 Å2-0 Å2
2---1.3808 Å20 Å2
3---2.7616 Å2
Refinement stepCycle: LAST / Resolution: 3→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9645 0 236 0 9881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610039
X-RAY DIFFRACTIONf_angle_d1.09313600
X-RAY DIFFRACTIONf_dihedral_angle_d17.4933680
X-RAY DIFFRACTIONf_chiral_restr0.071521
X-RAY DIFFRACTIONf_plane_restr0.0041727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.03510.35041470.29151460X-RAY DIFFRACTION96
3.0351-3.07080.35031720.25861459X-RAY DIFFRACTION100
3.0708-3.10820.25951750.23811457X-RAY DIFFRACTION100
3.1082-3.14750.24991320.22861501X-RAY DIFFRACTION100
3.1475-3.18890.26561630.22331502X-RAY DIFFRACTION100
3.1889-3.23260.32611790.23411454X-RAY DIFFRACTION100
3.2326-3.27880.31371580.23241479X-RAY DIFFRACTION100
3.2788-3.32770.25421580.21991498X-RAY DIFFRACTION100
3.3277-3.37970.25991640.21351478X-RAY DIFFRACTION100
3.3797-3.43510.28511710.2241481X-RAY DIFFRACTION100
3.4351-3.49430.24221720.20191481X-RAY DIFFRACTION100
3.4943-3.55790.24581740.22011477X-RAY DIFFRACTION100
3.5579-3.62630.26931570.20881503X-RAY DIFFRACTION100
3.6263-3.70030.25581790.20421472X-RAY DIFFRACTION100
3.7003-3.78070.23731510.2091501X-RAY DIFFRACTION100
3.7807-3.86860.2411700.19591479X-RAY DIFFRACTION100
3.8686-3.96530.2271580.18351510X-RAY DIFFRACTION100
3.9653-4.07250.22921800.19141482X-RAY DIFFRACTION100
4.0725-4.19220.21560.17651504X-RAY DIFFRACTION100
4.1922-4.32750.19461970.16951472X-RAY DIFFRACTION100
4.3275-4.4820.20092050.16581474X-RAY DIFFRACTION100
4.482-4.66130.1831800.15781492X-RAY DIFFRACTION100
4.6613-4.87330.19221550.17611518X-RAY DIFFRACTION100
4.8733-5.130.22591450.19921548X-RAY DIFFRACTION100
5.13-5.4510.22471860.22471501X-RAY DIFFRACTION100
5.451-5.87120.25971890.22681511X-RAY DIFFRACTION100
5.8712-6.46080.28161620.22811544X-RAY DIFFRACTION100
6.4608-7.39290.2161740.19811545X-RAY DIFFRACTION100
7.3929-9.30360.19761510.16521599X-RAY DIFFRACTION100
9.3036-48.66080.21771880.22941676X-RAY DIFFRACTION99

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