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- PDB-2rje: Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 1... -

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Basic information

Entry
Database: PDB / ID: 2rje
TitleCrystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), orthorhombic form II
Components
  • Histone H4
  • Lethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / L(3)MBT-LIKE PROTEIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger / Chromosomal protein / Methylation / Nucleosome core
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin formation / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / methylated histone binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / regulation of cell cycle / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus
Similarity search - Function
: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / SH3 type barrels. / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H4 / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAllali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: L3MBTL1 recognition of mono- and dimethylated histones.
Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H.
History
DepositionOct 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Aug 30, 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_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Lethal(3)malignant brain tumor-like protein
B: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
P: Histone H4
Q: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1767
Polymers116,1055
Non-polymers712
Water17,114950
1
A: Lethal(3)malignant brain tumor-like protein
Q: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2123
Polymers39,1772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lethal(3)malignant brain tumor-like protein
P: Histone H4


Theoretical massNumber of molelcules
Total (without water)39,1772
Polymers39,1772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lethal(3)malignant brain tumor-like protein
B: Lethal(3)malignant brain tumor-like protein
P: Histone H4
Q: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3895
Polymers78,3544
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7872
Polymers37,7511
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.894, 124.640, 90.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-592-

HOH

21B-639-

HOH

31B-762-

HOH

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein / L(3)mbt-like / L(3)mbt protein homolog / H-l(3)mbt protein / H-L(3)MBT / L3MBTL1


Mass: 37751.211 Da / Num. of mol.: 3 / Fragment: Residues 200-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468
#2: Protein/peptide Histone H4 /


Mass: 1425.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P62805*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 6% PEG 3350, 0.1M Ammonium sulfate, 20% Glycerol, 0.1 M Sodium acetate pH 4.4 , VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 2006 / Details: varimax
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→37.48 Å / Num. all: 103400 / Num. obs: 103400 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.085

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQW

2pqw


Resolution: 1.86→37.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.02 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23131 5159 5 %RANDOM
Rwork0.19086 ---
obs0.19292 98168 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.86→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7746 0 2 950 8698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218054
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.92410997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.87923.632402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.863151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6981540
X-RAY DIFFRACTIONr_chiral_restr0.1090.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026408
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23614
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25312
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0061.54903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55527778
X-RAY DIFFRACTIONr_scbond_it2.32333726
X-RAY DIFFRACTIONr_scangle_it3.4734.53219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 317 -
Rwork0.32 6469 -
obs--89.13 %

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